Yeast organism producing isobutanol at a high yield

ABSTRACT

The present invention provides recombinant microorganisms comprising an isobutanol producing metabolic pathway and methods of using said recombinant microorganisms to produce isobutanol. In various aspects of the invention, the recombinant microorganisms may comprise a modification resulting in the reduction of pyruvate decarboxylase and/or glycerol-3-phosphate dehydrogenase activity. In various embodiments described herein, the recombinant microorganisms may be microorganisms of the  Saccharomyces  clade, Crabtree-negative yeast microorganisms, Crabtree-positive yeast microorganisms, post-WGD (whole genome duplication) yeast microorganisms, pre-WGD (whole genome duplication) yeast microorganisms, and non-fermenting yeast microorganisms.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser.No. 12/820,505, filed Jun. 22, 2010, which claims priority to U.S.Provisional Application Ser. No. 61/219,173, filed Jun. 22, 2009. U.S.application Ser. No. 12/820,505 is also a continuation-in-part of U.S.application Ser. No. 12/696,645, filed Jan. 29, 2010, which is adivisional application of U.S. application Ser. No. 12/343,375, filedDec. 23, 2008, now U.S. Pat. No. 8,017,375, which claims, as does thepresent application, the benefit of U.S. Provisional Application Ser.No. 61/016,483, filed Dec. 23, 2007, all of which are hereinincorporated by reference in their entireties for all purposes.

TECHNICAL FIELD

Metabolically engineered microorganisms and methods of producing suchorganisms are provided. Also provided are methods of producingmetabolites that are biofuels by contacting a suitable substrate withmetabolically engineered microorganisms and enzymatic preparations therefrom.

DESCRIPTION OF THE TEXT FILE SUBMITTED ELECTRONICALLY

The contents of the text file submitted electronically herewith areincorporated herein by reference in their entirety: A computer readableformat copy of the Sequence Listing (filename:GEVO_(—)027_(—)06US_SeqList_ST25.txt, date recorded: Oct. 5, 2011, filesize: 438 kilobytes).

BACKGROUND

Biofuels have a long history ranging back to the beginning of the 20thcentury. As early as 1900, Rudolf Diesel demonstrated at the WorldExhibition in Paris, France, an engine running on peanut oil. Soonthereafter, Henry Ford demonstrated his Model T running on ethanolderived from corn. Petroleum-derived fuels displaced biofuels in the1930s and 1940s due to increased supply, and efficiency at a lower cost.

Market fluctuations in the 1970s coupled to the decrease in US oilproduction led to an increase in crude oil prices and a renewed interestin biofuels. Today, many interest groups, including policy makers,industry planners, aware citizens, and the financial community, areinterested in substituting petroleum-derived fuels with biomass-derivedbiofuels. The leading motivations for developing biofuels are ofeconomical, political, and environmental nature.

One is the threat of ‘peak oil’, the point at which the consumption rateof crude oil exceeds the supply rate, thus leading to significantlyincreased fuel cost results in an increased demand for alternativefuels. In addition, instability in the Middle East and other oil-richregions has increased the demand for domestically produced biofuels.Also, environmental concerns relating to the possibility of carbondioxide related climate change is an important social and ethicaldriving force which is starting to result in government regulations andpolicies such as caps on carbon dioxide emissions from automobiles,taxes on carbon dioxide emissions, and tax incentives for the use ofbiofuels.

Ethanol is the most abundant fermentatively produced fuel today but hasseveral drawbacks when compared to gasoline. Butanol, in comparison, hasseveral advantages over ethanol as a fuel: it can be made from the samefeedstocks as ethanol but, unlike ethanol, it is compatible withgasoline at any ratio and can also be used as a pure fuel in existingcombustion engines without modifications. Unlike ethanol, butanol doesnot absorb water and can thus be stored and distributed in the existingpetrochemical infrastructure. Due to its higher energy content which isclose to that of gasoline, the fuel economy (miles per gallon) is betterthan that of ethanol. Also, butanol-gasoline blends have lower vaporpressure than ethanol-gasoline blends, which is important in reducingevaporative hydrocarbon emissions.

Isobutanol has the same advantages as butanol with the additionaladvantage of having a higher octane number due to its branched carbonchain. Isobutanol is also useful as a commodity chemical and is also aprecursor to isobutylene and isobutylene-derived fuels and chemicals.Isobutanol has been produced recombinantly in yeast microorganismsexpressing a heterologous metabolic pathway (See, e.g., WO/2007/050671to Donaldson et al., and WO/2008/098227 to Liao et al.). However, theseyeast microorganisms fall short of commercial relevance due to their lowperformance characteristics, including low productivity, low titer, lowyield, and the requirement for oxygen during the fermentation process.One of the primary reasons for the sub-optimal performance observed inexisting isobutanol-producing microorganisms is the undesirableconversion of pathway intermediates to unwanted by-products.

Thus, there is an existing need to identify and reduce and/or eliminatethe metabolic processes catalyzing the conversion of isobutanol pathwayintermediates to unwanted by-products. The present inventors haveaddressed this need by providing recombinant microorganisms with reducedpyruvate decarboxylase (PDC) activity and reduced glycerol-3-phosphatedehydrogenase (GPD) activity.

SUMMARY OF THE INVENTION

The present inventors have observed that by combining the expression ofa cytosolically localized acetolactate synthase enzyme with reducedpyruvate decarboxylase (PDC) activity and/or reducedglycerol-3-phosphate dehydrogenase (GPD) activity, an unexpectedly highflux from pyruvate to acetolactate can be achieved. Thus, the inventionprovides yeast cells that are engineered to exhibit an efficientconversion of pyruvate to acetolactate in the cytoplasm due tosuppression of competing metabolic pathways. Therefore, as would beunderstood in the art, the present invention has utility for theproduction of any acetolactate-derived product, including, but notlimited to, isobutanol, 2-butanol, 1-butanol, 2-butanone,2,3-butanediol, valine, leucine, and 3-methyl-1-butanol.

Accordingly, in a first aspect, the invention provides a recombinantmicroorganism, such as a yeast cell, comprising acytosolically-localized polypeptide having acetolactate synthaseactivity wherein the yeast cell is substantially free of an enzymehaving pyruvate decarboxylase (PDC) activity and/or glycerol-3-phosphatedehydrogenase (GPD) activity, and wherein the cell converts pyruvate toacetolactate.

Thus, in various embodiments described herein, the present inventionprovides recombinant microorganisms engineered to include reducedpyruvate decarboxylase (PDC) activity as compared to a parentalmicroorganism. In one embodiment, PDC activity is eliminated. PDCcatalyzes the decarboxylation of pyruvate to acetaldehyde, which isreduced to ethanol by alcohol dehydrogenases via the oxidation of NADHto NAD+. In one embodiment, the recombinant microorganism includes amutation in at least one PDC gene resulting in a reduction of PDCactivity of a polypeptide encoded by said gene. In another embodiment,the recombinant microorganism includes a partial deletion of a PDC generesulting in a reduction of PDC activity of a polypeptide encoded bysaid gene. In another embodiment, the recombinant microorganismcomprises a complete deletion of a PDC gene resulting in a reduction ofPDC activity of a polypeptide encoded by said gene. In yet anotherembodiment, the recombinant microorganism includes a modification of theregulatory region associated with at least one PDC gene resulting in areduction of PDC activity of a polypeptide encoded by said gene. In yetanother embodiment, the recombinant microorganism comprises amodification of the transcriptional regulator resulting in a reductionof PDC gene transcription. In yet another embodiment, the recombinantmicroorganism comprises mutations in all PDC genes resulting in areduction of PDC activity of the polypeptides encoded by said genes. Inanother embodiment, the recombinant microorganism includes partialdeletions of all PDC genes resulting in a reduction of PDC activity ofthe polypeptides encoded by said genes. In yet another embodiment, therecombinant microorganism comprises a deletion of all PDC genesresulting in the elimination of PDC activity of the polypeptides encodedby said genes.

In additional embodiments, the present invention provides recombinantmicroorganisms engineered to exhibit reduced glycerol-3-phosphatedehydrogenase (GPD) activity as compared to a parental microorganism. Inone embodiment, GPD activity is eliminated. GPD catalyzes the reductionof dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate (G3P) viathe oxidation of NADH to NAD⁺. Glycerol is produced from G3P byGlycerol-3-phosphatase (GPP). In one embodiment, the recombinantmicroorganism includes a mutation in at least one GPD gene resulting ina reduction of GPD activity of a polypeptide encoded by said gene. Inanother embodiment, the recombinant microorganism includes a partialdeletion of a GPD gene resulting in a reduction of GPD activity of apolypeptide encoded by the gene. In another embodiment, the recombinantmicroorganism comprises a complete deletion of a GPD gene resulting in areduction of GPD activity of a polypeptide encoded by the gene. In yetanother embodiment, the recombinant microorganism includes amodification of the regulatory region associated with at least one GPDgene resulting in a reduction of GPD activity of a polypeptide encodedby said gene. In yet another embodiment, the recombinant microorganismcomprises a modification of the transcriptional regulator resulting in areduction of GPD gene transcription. In another embodiment, therecombinant microorganism includes partial deletions of all GPD genesresulting in a reduction of GPD activity of the polypeptides encoded bysaid genes. In yet another embodiment, the recombinant microorganismcomprises mutations in all GPD genes resulting in a reduction of GPDactivity of the polypeptides encoded by said genes. In yet anotherembodiment, the recombinant microorganism comprises a deletion of allGPD genes resulting in the elimination of GPD activity of thepolypeptides encoded by said genes.

In an exemplary embodiment, the present invention provides a recombinantmicroorganism engineered to exhibit reduced pyruvate decarboxylase (PDC)activity and reduced glycerol-3-phosphate dehydrogenase (GPD) activityas compared to a parental microorganism.

In additional embodiments, the present invention provides recombinantmicroorganisms engineered to exhibit reduced pyruvate dehydrogenase(PDH) activity as compared to a parental microorganism. In oneembodiment, the recombinant microorganism is engineered to have reducedpyruvate decarboxylase (PDC) activity and reduced pyruvate dehydrogenase(PDH) activity. In another embodiment, the recombinant microorganism isengineered to have reduced glycerol-3-phosphate dehydrogenase (GPD)activity and reduced pyruvate dehydrogenase (PDH) activity. In yetanother embodiment, the recombinant microorganism is engineered to havereduced pyruvate decarboxylase (PDC) activity, reducedglycerol-3-phosphate dehydrogenase (GPD) activity, and reduced pyruvatedehydrogenase (PDH) activity.

In various embodiments described herein, the present invention providesrecombinant microorganisms, including, but not limited to those, thatcomprise an isobutanol producing metabolic pathway. In some embodiments,the recombinant microorganisms can be engineered to express anisobutanol producing metabolic pathway comprising at least one exogenousgene that catalyzes a step in the conversion of pyruvate to isobutanol.In one embodiment, the recombinant microorganism may be engineered toexpress an isobutanol producing metabolic pathway comprising at leasttwo exogenous genes. In another embodiment, the recombinantmicroorganism may be engineered to express an isobutanol producingmetabolic pathway comprising at least three exogenous genes. In anotherembodiment, the recombinant microorganism may be engineered to expressan isobutanol producing metabolic pathway comprising at least fourexogenous genes. In another embodiment, the recombinant microorganismmay be engineered to express an isobutanol producing metabolic pathwaycomprising five exogenous genes.

In various embodiments described herein, isobutanol producing metabolicpathway comprises at least one exogenous gene that catalyzes a step inthe conversion of pyruvate to isobutanol. In one embodiment, theexogenous gene encodes a polypeptide selected from the group consistingof acetolactate synthase (ALS), ketol-acid reductoisomerase (KARI),dihydroxyacid dehydratase (DHAD), 2-keto-acid decarboxylase (KIVD), andalcohol dehydrogenase (ADH). In another embodiment, the exogenous geneencodes an acetolactate synthase (ALS). In an exemplary embodiment, theacetolactate synthase is a cytosolically-localized acetolactatesynthase. In one specific embodiment, the cytosolically-localizedacetolactate synthase is encoded by the Lactococcus lactis gene alsS. Inanother specific embodiment, the cytosolically-localized acetolactatesynthase is encoded by the Bacillus subtilis gene alsS.

In additional embodiments, the recombinant microorganism comprises anisobutanol producing metabolic pathway comprising genes encoding anNADH-dependent KARI and an NADH-dependent ADH. In one embodiment, theKARI and/or the ADH show at least a 10-fold higher catalytic efficiencyusing NADH as the cofactor as compared to the wild-type E. coli KARIilvC and a native E. coli ADH yqhD, respectively. In another embodiment,the KARI and/or the ADH have been modified or mutated to beNADH-dependent. In yet another embodiment, the KARI and/or the ADH hasbeen identified in nature with increased activity using NADH as acofactor as compared to the wild-type E. coli KARI ilvC and a native E.coli ADH yqhD, respectively.

In some embodiments, the invention provides a recombinant microorganismcomprising an isobutanol producing metabolic pathway, wherein saidrecombinant microorganism comprises a reduction in pyruvatedecarboxylase (PDC) activity as compared to a parental microorganism. Inadditional embodiments, the recombinant microorganism comprises areduction in glycerol-3-phosphate dehydrogenase (GPD) activity ascompared to a parental microorganism. In yet other embodiments, therecombinant microorganism comprises a reduction in pyruvatedecarboxylase (PDC) activity and glycerol-3-phosphate dehydrogenase(GPD) activity as compared to a parental microorganism. In still yetother embodiments, the recombinant microorganism comprises a reductionin pyruvate decarboxylase (PDC) activity, a reduction inglycerol-3-phosphate dehydrogenase (GPD) activity, and a reduction inpyruvate dehydrogenase (PDH) activity as compared to a parentalmicroorganism.

In various embodiments described herein, the present invention providesrecombinant microorganisms that comprise a pathway for the fermentationof isobutanol from a pentose sugar. In one embodiment, the pentose sugaris xylose. In one embodiment, the recombinant microorganism isengineered to express a functional xylose isomerase (XI). In anotherembodiment, the recombinant microorganism further comprises a deletionor disruption of a native gene encoding for an enzyme that catalyzes theconversion of xylose to xylitol. In one embodiment, the native gene isxylose reductase (XR). In another embodiment, the native gene is xylitoldehydrogenase (XDH). In yet another embodiment, both native genes aredeleted or disrupted. In yet another embodiment, the recombinantmicroorganism further engineered to express, xylulose kinase whichcatalyzes the conversion of xylulose to xylulose-5-phosphate.

In some embodiments, the microorganisms of the present invention areengineered to grow on glucose independently of C2-compounds at a growthrate substantially equivalent to the growth rate of a parentalmicroorganism without altered PDC activity.

In various embodiments described herein, the recombinant microorganismsmay be microorganisms of the Saccharomyces clade, Saccharomyces sensustrict microorganisms, Crabtree-negative yeast microorganisms,Crabtree-positive yeast microorganisms, post-WGD (whole genomeduplication) yeast microorganisms, pre-WGD (whole genome duplication)yeast microorganisms, and non-fermenting yeast microorganisms.

In some embodiments, the recombinant microorganisms may be yeastrecombinant microorganisms of the Saccharomyces clade.

In some embodiments, the recombinant microorganisms may be Saccharomycessensu stricto microorganisms. In one embodiment, the Saccharomyces sensustricto is selected from the group consisting of S. cerevisiae, S.kudriavzevii, S. mikatae, S. bayanus, S. uvarum, S. carocanis andhybrids thereof.

In some embodiments, the recombinant microorganisms may beCrabtree-negative recombinant yeast microorganisms. In one embodiment,the Crabtree-negative yeast microorganism is classified into a generaselected from the group consisting of Kluyveromyces, Pichia, Hansenula,or Candida. In additional embodiments, the Crabtree-negative yeastmicroorganism is selected from Kluyveromyces lactis, Kluyveromycesmarxianus, Pichia anomala, Pichia stipitis, P. kudriavzevii, Hansenulaanomala, Candida utilis and Kluyveromyces waltii.

In some embodiments, the recombinant microorganisms may beCrabtree-positive recombinant yeast microorganisms. In one embodiment,the Crabtree-positive yeast microorganism is classified into a generaselected from the group consisting of Saccharomyces, Kluyveromyces,Zygosaccharomyces, Debaryomyces, Candida, Pichia andSchizosaccharomyces. In additional embodiments, the Crabtree-positiveyeast microorganism is selected from the group consisting ofSaccharomyces cerevisiae, Saccharomyces uvarum, Saccharomyces bayanus,Saccharomyces paradoxus, Saccharomyces castelli, Saccharomyces kluyveri,Kluyveromyces thermotolerans, Candida glabrata, Z. bailli, Z. rouxii,Debaryomyces hansenii, Pichia pastorius, Schizosaccharomyces pombe, andSaccharomyces uvarum.

In some embodiments, the recombinant microorganisms may be post-WGD(whole genome duplication) yeast recombinant microorganisms. In oneembodiment, the post-WGD yeast recombinant microorganism is classifiedinto a genera selected from the group consisting of Saccharomyces orCandida. In additional embodiments, the post-WGD yeast is selected fromthe group consisting of Saccharomyces cerevisiae, Saccharomyces uvarum,Saccharomyces bayanus, Saccharomyces paradoxus, Saccharomyces castelli,and Candida glabrata.

In some embodiments, the recombinant microorganisms may be pre-WGD(whole genome duplication) yeast recombinant microorganisms. In oneembodiment, the pre-WGD yeast recombinant microorganism is classifiedinto a genera selected from the group consisting of Saccharomyces,Kluyveromyces, Candida, Pichia, Debaryomyces, Hansenula, Pachysolen,Yarrowia and Schizosaccharomyces. In additional embodiments, the pre-WGDyeast is selected from the group consisting of Saccharomyces kluyveri,Kluyveromyces thermotolerans, Kluyveromyces marxianus, Kluyveromyceswaltii, Kluyveromyces lactis, Candida tropicalis, Pichia pastoris,Pichia anomala, Pichia stipitis, Debaryomyces hansenii, Hansenulaanomala, Pachysolen tannophilis, Yarrowia lipolytica, andSchizosaccharomyces pombe.

In some embodiments, the recombinant microorganisms may bemicroorganisms that are non-fermenting yeast microorganisms, including,but not limited to those, classified into a genera selected from thegroup consisting of Tricosporon, Rhodotorula, or Myxozyma.

In another aspect, the present invention provides methods of producingisobutanol using a recombinant microorganism of the invention. In oneembodiment, the method includes cultivating the recombinantmicroorganism in a culture medium containing a feedstock providing thecarbon source until a recoverable quantity of the isobutanol is producedand optionally, recovering the isobutanol. In one embodiment, themicroorganism is selected to produce isobutanol from a carbon source ata yield of at least about 5 percent theoretical. In another embodiment,the microorganism is selected to produce isobutanol at a yield of atleast about 10 percent, at least about 15 percent, about least about 20percent, at least about 25 percent, at least about 30 percent, at leastabout 35 percent, at least about 40 percent, at least about 45 percent,at least about 50 percent, at least about 55 percent, at least about 60percent, at least about 65 percent, at least about 70 percent, at leastabout 75 percent, at least about 80 percent, at least about 85 percent,at least about 90 percent, or at least about 95 percent theoretical.

In one embodiment, the microorganism is selected to produce isobutanolfrom a carbon source at a specific productivity of at least about 0.7mg/L/hr per OD. In another embodiment, the microorganism is selected toproduce isobutanol from a carbon source at a specific productivity of atleast about 1 mg/L/hr per OD, at least about 10 mg/L/hr per OD, at leastabout 50 mg/L/hr per OD, at least about 100 mg/L/hr per OD, at leastabout 250 mg/L/hr per OD, or at least about 500 mg/L/hr per OD.

BRIEF DESCRIPTION OF DRAWINGS

Illustrative embodiments of the invention are illustrated in thedrawings, in which:

FIG. 1 illustrates an exemplary embodiment of an isobutanol pathway.

FIG. 2 illustrates production of pyruvate via glycolysis, together withan isobutanol pathway which converts pyruvate to isobutanol and a PDCpathway which converts pyruvate to acetaldehyde and carbon dioxide.

FIG. 3 illustrates an isobutanol pathway receiving additional pyruvateto form isobutanol at higher yield due to the deletion or reduction ofthe PDC pathway.

FIG. 4 illustrates an isobutanol pathway receiving additional pyruvateto form isobutanol at higher yield due to deletion or reduction of thePDC pathway and the deletion or reduction of the GPD pathway.

FIG. 5 illustrates the carbon source composition and feeding rate overtime during chemostat evolution of the S. cerevisiae Pdc-minus strainGEVO1584. This graph shows how the acetate was decreased over a periodof 480 hours from 0.375 g/L to 0 g/L. It also shows the total feedingrate. Higher feeding rate meant that growth rate was higher. Since thechemostat contained 200 ml of culture, dilution rate can be calculatedby dividing the feeding rate by 200 ml.

FIG. 6 illustrates growth of evolved Pdc-minus mutant strain GEVO1863 inYPD compared to the parental strain, GEVO1187.

FIG. 7 illustrates that the evolved PDC mutant, GEVO1863, does notproduce ethanol in YPD medium, unlike the parental strain GEVO1187.

FIG. 8 illustrates a schematic map of plasmid pGV1503.

FIG. 9 illustrates a schematic map of plasmid pGV1537.

FIG. 10 illustrates a schematic map of plasmid pGV1429.

FIG. 11 illustrates a schematic map of plasmid pGV1430.

FIG. 12 illustrates a schematic map of plasmid pGV1431.

FIG. 13 illustrates a schematic map of plasmid pGV1472.

FIG. 14 illustrates a schematic map of plasmid pGV1473.

FIG. 15 illustrates a schematic map of plasmid pGV1475.

FIG. 16 illustrates a schematic map of plasmid pGV1254.

FIG. 17 illustrates a schematic map of plasmid pGV1295.

FIG. 18 illustrates a schematic map of plasmid pGV1390.

FIG. 19 illustrates a schematic map of plasmid pGV1438.

FIG. 20 illustrates a schematic map of plasmid pGV1590.

FIG. 21 illustrates a schematic map of plasmid pGV1726.

FIG. 22 illustrates a schematic map of plasmid pGV1727.

FIG. 23 illustrates a schematic map of plasmid pGV1056.

FIG. 24 illustrates a schematic map of plasmid pGV1062.

FIG. 25 illustrates a schematic map of plasmid pGV1102.

FIG. 26 illustrates a schematic map of plasmid pGV1103.

FIG. 27 illustrates a schematic map of plasmid pGV1104.

FIG. 28 illustrates a schematic map of plasmid pGV1106.

FIG. 29 illustrates a schematic map of plasmid pGV1649.

FIG. 30 illustrates a schematic map of plasmid pGV1664.

FIG. 31 illustrates a schematic map of plasmid pGV1672.

FIG. 32 illustrates a schematic map of plasmid pGV1673.

FIG. 33 illustrates a schematic map of plasmid pGV1677.

FIG. 34 illustrates a schematic map of plasmid pGV1679.

FIG. 35 illustrates a schematic map of plasmid pGV1683.

FIG. 36 illustrates a schematic map of plasmid pGV1565.

FIG. 37 illustrates a schematic map of plasmid pGV1568.

FIG. 38 illustrates a schematic map of plasmid pGV2082.

FIG. 39 illustrates a schematic map of plasmid pGV2114.

FIG. 40 illustrates a schematic map of plasmid pGV2117.

FIG. 41 illustrates a schematic map of plasmid pGV2118.

DETAILED DESCRIPTION

As used herein and in the appended claims, the singular forms “a,” “an,”and “the” include plural referents unless the context clearly dictatesotherwise. Thus, for example, reference to “a polynucleotide” includes aplurality of such polynucleotides and reference to “the microorganism”includes reference to one or more microorganisms, and so forth.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which this disclosure belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice of the disclosed methods and compositions, the exemplarymethods, devices and materials are described herein.

Any publications discussed above and throughout the text are providedsolely for their disclosure prior to the filing date of the presentapplication. Nothing herein is to be construed as an admission that theinventors are not entitled to antedate such disclosure by virtue ofprior disclosure.

The term “microorganism” includes prokaryotic and eukaryotic microbialspecies from the Domains Archaea, Bacteria and Eucarya, the latterincluding yeast and filamentous fungi, protozoa, algae, or higherProtista. The terms “microbial cells” and “microbes” are usedinterchangeably with the term microorganism.

“Bacteria”, or “eubacteria”, refers to a domain of prokaryoticorganisms. Bacteria include at least 11 distinct groups as follows: (1)Gram-positive (gram+) bacteria, of which there are two majorsubdivisions: (1) high G+C group (Actinomycetes, Mycobacteria,Micrococcus, others) (2) low G+C group (Bacillus, Clostridia,Lactobacillus, Staphylococci, Streptococci, Mycoplasmas); (2)Proteobacteria, e.g., Purple photosynthetic +non-photosyntheticGram-negative bacteria (includes most “common” Gram-negative bacteria);(3) Cyanobacteria, e.g., oxygenic phototrophs; (4) Spirochetes andrelated species; (5) Planctomyces; (6) Bacteroides, Flavobacteria; (7)Chlamydia; (8) Green sulfur bacteria; (9) Green non-sulfur bacteria(also anaerobic phototrophs); (10) Radioresistant micrococci andrelatives; (11) Thermotoga and Thermosipho thermophiles.

“Gram-negative bacteria” include cocci, nonenteric rods, and entericrods. The genera of Gram-negative bacteria include, for example,Neisseria, Spirillum, Pasteurella, Brucella, Yersinia, Francisella,Haemophilus, Bordetella, Escherichia, Salmonella, Shigella, Klebsiella,Proteus, Vibrio, Pseudomonas, Bacteroides, Acetobacter, Aerobacter,Agrobacterium, Azotobacter, Spirilla, Serratia, Vibrio, Rhizobium,Chlamydia, Rickettsia, Treponema, and Fusobacterium.

“Gram positive bacteria” include cocci, nonsporulating rods, andsporulating rods. The genera of gram positive bacteria include, forexample, Actinomyces, Bacillus, Clostridium, Corynebacterium,Erysipelothrix, Lactobacillus, Listeria, Mycobacterium, Myxococcus,Nocardia, Staphylococcus, Streptococcus, and Streptomyces.

The term “genus” is defined as a taxonomic group of related speciesaccording to the Taxonomic Outline of Bacteria and Archaea (Garrity, G.M., Lilburn, T. G., Cole, J. R., Harrison, S. H., Euzeby, J., andTindall, B. J. (2007) The Taxonomic Outline of Bacteria and Archaea.TOBA Release 7.7, March 2007. Michigan State University Board ofTrustees.

The term “species” is defined as a collection of closely relatedorganisms with greater than 97% 16S ribosomal RNA sequence homology andgreater than 70% genomic hybridization and sufficiently different fromall other organisms so as to be recognized as a distinct unit.

The term “recombinant microorganism,” “modified microorganism,” and“recombinant host cell” are used interchangeably herein and refer tomicroorganisms that have been genetically modified to express orover-express endogenous polynucleotides, or to express heterologouspolynucleotides, such as those included in a vector, or which have analteration in expression of an endogenous gene. By “alteration” it ismeant that the expression of the gene, or level of a RNA molecule orequivalent RNA molecules encoding one or more polypeptides orpolypeptide subunits, or activity of one or more polypeptides orpolypeptide subunits is up regulated or down regulated, such thatexpression, level, or activity is greater than or less than thatobserved in the absence of the alteration. For example, the term “alter”can mean “inhibit,” but the use of the word “alter” is not limited tothis definition.

The term “expression” with respect to a gene sequence refers totranscription of the gene and, as appropriate, translation of theresulting mRNA transcript to a protein. Thus, as will be clear from thecontext, expression of a protein results from transcription andtranslation of the open reading frame sequence. The level of expressionof a desired product in a host cell may be determined on the basis ofeither the amount of corresponding mRNA that is present in the cell, orthe amount of the desired product encoded by the selected sequence. Forexample, mRNA transcribed from a selected sequence can be quantitated byPCR or by northern hybridization (see Sambrook et al., MolecularCloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press(1989)). Protein encoded by a selected sequence can be quantitated byvarious methods, e.g., by ELISA, by assaying for the biological activityof the protein, or by employing assays that are independent of suchactivity, such as western blotting or radioimmunoassay, using antibodiesthat are recognize and bind reacting the protein. See Sambrook et al.,1989, supra. The polynucleotide generally encodes a target enzymeinvolved in a metabolic pathway for producing a desired metabolite. Itis understood that the terms “recombinant microorganism” and“recombinant host cell” refer not only to the particular recombinantmicroorganism but to the progeny or potential progeny of such amicroorganism. Because certain modifications may occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

The term “wild-type microorganism” describes a cell that occurs innature, i.e. a cell that has not been genetically modified. A wild-typemicroorganism can be genetically modified to express or overexpress afirst target enzyme. This microorganism can act as a parentalmicroorganism in the generation of a microorganism modified to expressor overexpress a second target enzyme. In turn, the microorganismmodified to express or overexpress a first and a second target enzymecan be modified to express or overexpress a third target enzyme.

Accordingly, a “parental microorganism” functions as a reference cellfor successive genetic modification events. Each modification event canbe accomplished by introducing a nucleic acid molecule in to thereference cell. The introduction facilitates the expression oroverexpression of a target enzyme. It is understood that the term“facilitates” encompasses the activation of endogenous polynucleotidesencoding a target enzyme through genetic modification of e.g., apromoter sequence in a parental microorganism. It is further understoodthat the term “facilitates” encompasses the introduction of heterologouspolynucleotides encoding a target enzyme in to a parental microorganism

The term “engineer” refers to any manipulation of a microorganism thatresult in a detectable change in the microorganism, wherein themanipulation includes but is not limited to inserting a polynucleotideand/or polypeptide heterologous to the microorganism and mutating apolynucleotide and/or polypeptide native to the microorganism. The term“metabolically engineered” or “metabolic engineering” involves rationalpathway design and assembly of biosynthetic genes, genes associated withoperons, and control elements of such polynucleotides, for theproduction of a desired metabolite. “Metabolically engineered” canfurther include optimization of metabolic flux by regulation andoptimization of transcription, translation, protein stability andprotein functionality using genetic engineering and appropriate culturecondition including the reduction of, disruption, or knocking out of, acompeting metabolic pathway that competes with an intermediate leadingto a desired pathway.

The terms “metabolically engineered microorganism” and “modifiedmicroorganism” are used interchangeably herein and refer not only to theparticular subject cell but to the progeny or potential progeny of sucha cell. Because certain modifications may occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

The term “mutation” as used herein indicates any modification of anucleic acid and/or polypeptide which results in an altered nucleic acidor polypeptide. Mutations include, for example, point mutations,deletions, or insertions of single or multiple residues in apolynucleotide, which includes alterations arising within aprotein-encoding region of a gene as well as alterations in regionsoutside of a protein-encoding sequence, such as, but not limited to,regulatory or promoter sequences. A genetic alteration may be a mutationof any type. For instance, the mutation may constitute a point mutation,a frame-shift mutation, an insertion, or a deletion of part or all of agene. In addition, in some embodiments of the modified microorganism, aportion of the microorganism genome has been replaced with aheterologous polynucleotide. In some embodiments, the mutations arenaturally-occurring. In other embodiments, the mutations are the resultsof artificial selection pressure. In still other embodiments, themutations in the microorganism genome are the result of geneticengineering.

The term “biosynthetic pathway”, also referred to as “metabolicpathway”, refers to a set of anabolic or catabolic biochemical reactionsfor converting one chemical species into another. Gene products belongto the same “metabolic pathway” if they, in parallel or in series, acton the same substrate, produce the same product, or act on or produce ametabolic intermediate (i.e., metabolite) between the same substrate andmetabolite end product.

The term “heterologous” as used herein with reference to molecules andin particular enzymes and polynucleotides, indicates molecules that areexpressed in an organism other than the organism from which theyoriginated or are found in nature, independently of the level ofexpression that can be lower, equal or higher than the level ofexpression of the molecule in the native microorganism.

On the other hand, the term “native” or “endogenous” as used herein withreference to molecules, and in particular enzymes and polynucleotides,indicates molecules that are expressed in the organism in which theyoriginated or are found in nature, independently of the level ofexpression that can be lower equal or higher than the level ofexpression of the molecule in the native microorganism. It is understoodthat expression of native enzymes or polynucleotides may be modified inrecombinant microorganisms.

The term “feedstock” is defined as a raw material or mixture of rawmaterials supplied to a microorganism or fermentation process from whichother products can be made. For example, a carbon source, such asbiomass or the carbon compounds derived from biomass are a feedstock fora microorganism that produces a biofuel in a fermentation process.However, a feedstock may contain nutrients other than a carbon source.

The term “substrate” or “suitable substrate” refers to any substance orcompound that is converted or meant to be converted into anothercompound by the action of an enzyme. The term includes not only a singlecompound, but also combinations of compounds, such as solutions,mixtures and other materials which contain at least one substrate, orderivatives thereof. Further, the term “substrate” encompasses not onlycompounds that provide a carbon source suitable for use as a startingmaterial, such as any biomass derived sugar, but also intermediate andend product metabolites used in a pathway associated with ametabolically engineered microorganism as described herein.

The term “C2-compound” as used as a carbon source for engineered yeastmicroorganisms with mutations in all pyruvate decarboxylase (PDC) genesresulting in a reduction of pyruvate decarboxylase activity of saidgenes refers to organic compounds comprised of two carbon atoms,including but not limited to ethanol and acetate.

The term “fermentation” or “fermentation process” is defined as aprocess in which a microorganism is cultivated in a culture mediumcontaining raw materials, such as feedstock and nutrients, wherein themicroorganism converts raw materials, such as a feedstock, intoproducts. The term “cell dry weight” or “CDW” refers to the weight ofthe microorganism after the water contained in the microorganism hasbeen removed using methods known to one skilled in the art. CDW isreported in grams.

The term “biofuel” refers to a fuel in which all carbon contained withinthe fuel is derived from biomass and is biochemically converted, atleast in part, in to a fuel by a microorganism. A biofuel is furtherdefined as a non-ethanol compound which contains less than 0.5 oxygenatoms per carbon atom. A biofuel is a fuel in its own right, but may beblended with petroleum-derived fuels to generate a fuel. A biofuel maybe used as a replacement for petrochemically-derived gasoline, dieselfuel, or jet fuel.

The term “volumetric productivity” or “production rate” is defined asthe amount of product formed per volume of medium per unit of time.Volumetric productivity is reported in gram per liter per hour (g/L/h).

The term “specific productivity” or “specific production rate” isdefined as the amount of product formed per volume of medium per unit oftime per amount of cells. Volumetric productivity is reported in gram ormilligram per liter per hour per OD (g/L/h/OD).

The term “yield” is defined as the amount of product obtained per unitweight of raw material and may be expressed as g product per g substrate(g/g). Yield may be expressed as a percentage of the theoretical yield.“Theoretical yield” is defined as the maximum amount of product that canbe generated per a given amount of substrate as dictated by thestoichiometry of the metabolic pathway used to make the product. Forexample, the theoretical yield for one typical conversion of glucose toisobutanol is 0.41 g/g. As such, a yield of isobutanol from glucose of0.39 g/g would be expressed as 95% of theoretical or 95% theoreticalyield.

The term “titer” is defined as the strength of a solution or theconcentration of a substance in solution. For example, the titer of abiofuel in a fermentation broth is described as g of biofuel in solutionper liter of fermentation broth (g/L).

A “facultative anaerobic organism” or a “facultative anaerobicmicroorganism” is defined as an organism that can grow in either thepresence or in the absence of oxygen.

A “strictly anaerobic organism” or a “strictly anaerobic microorganism”is defined as an organism that cannot grow in the presence of oxygen andwhich does not survive exposure to any concentration of oxygen.

An “anaerobic organism” or an “anaerobic microorganism” is defined as anorganism that cannot grow in the presence of oxygen.

“Aerobic conditions” are defined as conditions under which the oxygenconcentration in the fermentation medium is sufficiently high for anaerobic or facultative anaerobic microorganism to use as a terminalelectron acceptor.

In contrast, “Anaerobic conditions” are defined as conditions underwhich the oxygen concentration in the fermentation medium is too low forthe microorganism to use as a terminal electron acceptor. Anaerobicconditions may be achieved by sparging a fermentation medium with aninert gas such as nitrogen until oxygen is no longer available to themicroorganism as a terminal electron acceptor. Alternatively, anaerobicconditions may be achieved by the microorganism consuming the availableoxygen of the fermentation until oxygen is unavailable to themicroorganism as a terminal electron acceptor. Methods for theproduction of isobutanol under anaerobic conditions are described incommonly owned and co-pending applications U.S. Ser. No. 12/610,784 andPCT/US09/62952 (published as WO/2010/051527), the disclosures of whichare herein incorporated by reference in their entireties for allpurposes.

“Aerobic metabolism” refers to a biochemical process in which oxygen isused as a terminal electron acceptor to make energy, typically in theform of ATP, from carbohydrates. Aerobic metabolism occurs e.g. viaglycolysis and the TCA cycle, wherein a single glucose molecule ismetabolized completely into carbon dioxide in the presence of oxygen.

In contrast, “anaerobic metabolism” refers to a biochemical process inwhich oxygen is not the final acceptor of electrons contained in NADH.Anaerobic metabolism can be divided into anaerobic respiration, in whichcompounds other than oxygen serve as the terminal electron acceptor, andsubstrate level phosphorylation, in which the electrons from NADH areutilized to generate a reduced product via a “fermentative pathway.”

In “fermentative pathways”, NAD(P)H donates its electrons to a moleculeproduced by the same metabolic pathway that produced the electronscarried in NAD(P)H. For example, in one of the fermentative pathways ofcertain yeast strains, NAD(P)H generated through glycolysis transfersits electrons to acetaldehyde, yielding ethanol. Fermentative pathwaysare usually active under anaerobic conditions but may also occur underaerobic conditions, under conditions where NADH is not fully oxidizedvia the respiratory chain. For example, above certain glucoseconcentrations, Crabtree-positive yeasts produce large amounts ofethanol under aerobic conditions.

The term “byproduct” or “by-product” means an undesired product relatedto the production of a biofuel or biofuel precursor. Byproducts aregenerally disposed as waste, adding cost to a production process.

The term “substantially free” when used in reference to the presence orabsence of enzymatic activities (PDC, GPD, PDH, etc.) in carbon pathwaysthat compete with the desired metabolic pathway (e.g. anisobutanol-producing metabolic pathway) means the level of the enzyme issubstantially less than that of the same enzyme in the wild-type host,wherein less than about 50% of the wild-type level is preferred and lessthan about 30% is more preferred. The activity may be less than about20%, less than about 10%, less than about 5%, or less than about 1% ofwild-type activity.

The term “non-fermenting yeast” is a yeast species that fails todemonstrate an anaerobic metabolism in which the electrons from NADH areutilized to generate a reduced product via a fermentative pathway suchas the production of ethanol and CO₂ from glucose. Non-fermentativeyeast can be identified by the “Durham Tube Test” (J. A. Barnett, R. W.Payne, and D. Yarrow. 2000. Yeasts Characteristics and Identification.3^(rd) edition. p. 28-29. Cambridge University Press, Cambridge, UK.) orby monitoring the production of fermentation productions such as ethanoland CO₂.

The term “polynucleotide” is used herein interchangeably with the term“nucleic acid” and refers to an organic polymer composed of two or moremonomers including nucleotides, nucleosides or analogs thereof,including but not limited to single stranded or double stranded, senseor antisense deoxyribonucleic acid (DNA) of any length and, whereappropriate, single stranded or double stranded, sense or antisenseribonucleic acid (RNA) of any length, including siRNA. The term“nucleotide” refers to any of several compounds that consist of a riboseor deoxyribose sugar joined to a purine or a pyrimidine base and to aphosphate group, and that are the basic structural units of nucleicacids. The term “nucleoside” refers to a compound (as guanosine oradenosine) that consists of a purine or pyrimidine base combined withdeoxyribose or ribose and is found especially in nucleic acids. The term“nucleotide analog” or “nucleoside analog” refers, respectively, to anucleotide or nucleoside in which one or more individual atoms have beenreplaced with a different atom or with a different functional group.Accordingly, the term polynucleotide includes nucleic acids of anylength, DNA, RNA, analogs and fragments thereof. A polynucleotide ofthree or more nucleotides is also called nucleotidic oligomer oroligonucleotide.

It is understood that the polynucleotides described herein include“genes” and that the nucleic acid molecules described herein include“vectors” or “plasmids.” Accordingly, the term “gene”, also called a“structural gene” refers to a polynucleotide that codes for a particularsequence of amino acids, which comprise all or part of one or moreproteins or enzymes, and may include regulatory (non-transcribed) DNAsequences, such as promoter sequences, which determine for example theconditions under which the gene is expressed. The transcribed region ofthe gene may include untranslated regions, including introns,5′-untranslated region (UTR), and 3′-UTR, as well as the codingsequence.

The term “operon” refers to two or more genes which are transcribed as asingle transcriptional unit from a common promoter. In some embodiments,the genes comprising the operon are contiguous genes. It is understoodthat transcription of an entire operon can be modified (i.e., increased,decreased, or eliminated) by modifying the common promoter.Alternatively, any gene or combination of genes in an operon can bemodified to alter the function or activity of the encoded polypeptide.The modification can result in an increase in the activity of theencoded polypeptide. Further, the modification can impart new activitieson the encoded polypeptide. Exemplary new activities include the use ofalternative substrates and/or the ability to function in alternativeenvironmental conditions.

A “vector” is any means by which a nucleic acid can be propagated and/ortransferred between organisms, cells, or cellular components. Vectorsinclude viruses, bacteriophage, pro-viruses, plasmids, phagemids,transposons, and artificial chromosomes such as YACs (yeast artificialchromosomes), BACs (bacterial artificial chromosomes), and PLACs (plantartificial chromosomes), and the like, that are “episomes,” that is,that replicate autonomously or can integrate into a chromosome of a hostcell. A vector can also be a naked RNA polynucleotide, a naked DNApolynucleotide, a polynucleotide composed of both DNA and RNA within thesame strand, a poly-lysine -conjugated DNA or RNA, a peptide-conjugatedDNA or RNA, a liposome-conjugated DNA, or the like, that are notepisomal in nature, or it can be an organism which comprises one or moreof the above polynucleotide constructs such as an agrobacterium or abacterium.

“Transformation” refers to the process by which a vector is introducedinto a host cell. Transformation (or transduction, or transfection), canbe achieved by any one of a number of means including chemicaltransformation (e.g. lithium acetate transformation), electroporation,microinjection, biolistics (or particle bombardment-mediated delivery),or agrobacterium mediated transformation.

The term “enzyme” as used herein refers to any substance that catalyzesor promotes one or more chemical or biochemical reactions, which usuallyincludes enzymes totally or partially composed of a polypeptide, but caninclude enzymes composed of a different molecule includingpolynucleotides.

The term “protein,” “peptide,” or “polypeptide” as used herein indicatesan organic polymer composed of two or more amino acidic monomers and/oranalogs thereof. As used herein, the term “amino acid” or “amino acidicmonomer” refers to any natural and/or synthetic amino acids includingglycine and both D or L optical isomers. The term “amino acid analog”refers to an amino acid in which one or more individual atoms have beenreplaced, either with a different atom, or with a different functionalgroup. Accordingly, the term polypeptide includes amino acidic polymerof any length including full length proteins, and peptides as well asanalogs and fragments thereof. A polypeptide of three or more aminoacids is also called a protein oligomer or oligopeptide

The term “homolog”, used with respect to an original enzyme or gene of afirst family or species, refers to distinct enzymes or genes of a secondfamily or species which are determined by functional, structural orgenomic analyses to be an enzyme or gene of the second family or specieswhich corresponds to the original enzyme or gene of the first family orspecies. Most often, homologs will have functional, structural orgenomic similarities. Techniques are known by which homologs of anenzyme or gene can readily be cloned using genetic probes and PCR.Identity of cloned sequences as homolog can be confirmed usingfunctional assays and/or by genomic mapping of the genes.

A protein has “homology” or is “homologous” to a second protein if thenucleic acid sequence that encodes the protein has a similar sequence tothe nucleic acid sequence that encodes the second protein.Alternatively, a protein has homology to a second protein if the twoproteins have “similar” amino acid sequences. (Thus, the term“homologous proteins” is defined to mean that the two proteins havesimilar amino acid sequences).

The term “analog” or “analogous” refers to nucleic acid or proteinsequences or protein structures that are related to one another infunction only and are not from common descent or do not share a commonancestral sequence. Analogs may differ in sequence but may share asimilar structure, due to convergent evolution. For example, two enzymesare analogs or analogous if the enzymes catalyze the same reaction ofconversion of a substrate to a product, are unrelated in sequence, andirrespective of whether the two enzymes are related in structure.

As used herein and as would be understood by one of ordinary skill inthe art, “reduced activity and/or expression” of an endogenous proteinsuch an enzyme can mean either a reduced specific catalytic activity ofthe protein (e.g. reduced activity) and/or decreased concentrations ofthe protein in the cell (e.g. reduced expression), while “deletedactivity and/or expression” of an endogenous protein such an enzyme canmean either no or negligible specific catalytic activity of the enzyme(e.g. deleted activity)and/or no or negligible concentrations of theenzyme in the cell (e.g. deleted expression).

The term “reduced pyruvate decarboxylase activity” means either adecreased concentration of the pyruvate decarboxylase enzyme in the cellor reduced or no specific catalytic activity of the pyruvatedecarboxylase enzyme.

The term “reduced glycerol-3-phosphate dehydrogenase activity” meanseither a decreased concentration of the glycerol-3-phosphatedehydrogenase enzyme in the cell or reduced or no specific catalyticactivity of the glycerol-3-phosphate dehydrogenase enzyme.

The term “reduced pyruvate dehydrogenase activity” means either adecreased concentration of the pyruvate dehydrogenase enzyme in the cellor reduced or no specific catalytic activity of the pyruvatedehydrogenase enzyme.

The term “reduced xylose reductase activity” means either a decreasedconcentration of the xylose reductase enzyme in the cell or reduced orno specific catalytic activity of the xylose reductase enzyme.

The term “reduced xylitol dehydrogenase activity” means either adecreased concentration of xylitol dehydrogenase enzyme in the cell orreduced or no specific catalytic activity of the xylitol dehydrogenaseenzyme.

The Microorganism in General

Native producers of 1-butanol, such as Clostridium acetobutylicum, areknown, but these organisms also generate byproducts such as acetone,ethanol, and butyrate during fermentations. Furthermore, thesemicroorganisms are relatively difficult to manipulate, withsignificantly fewer tools available than in more commonly usedproduction hosts such as E. coli and yeast (e.g. S. cerevisiae).

Yeast cells produce pyruvate from sugars, which is then utilized in anumber of pathways of cellular metabolism. Yeast cells can be engineeredto produce a number of desirable products with the initial biosyntheticpathway step being conversion of endogenous pyruvate to acetolactate.The present inventors have observed that by combining the expression ofa cytosolically localized acetolactate synthase enzyme with reducedpyruvate decarboxylase (PDC) activity and/or reducedglycerol-3-phosphate dehydrogenase (GPD) activity, an unexpectedly highflux from pyruvate to acetolactate can be achieved. Thus, the inventionprovides yeast cells that are engineered to exhibit an efficientconversion of pyruvate to acetolactate in the cytoplasm due tosuppression of competing metabolic pathways. Therefore, as would beunderstood in the art, the present invention has utility for theproduction of any acetolactate-derived product, including, but notlimited to, isobutanol, 2-butanol, 1-butanol, 2-butanone,2,3-butanediol, valine, leucine, and 3-methyl-1-butanol.

Engineered biosynthetic pathways for synthesis of isobutanol aredescribed in commonly owned and co-pending applications U.S. Ser. No.12/343,375 (published as US 2009/0226991), U.S. Ser. No. 12/696,645,U.S. Ser. No. 12/610,784, PCT/US09/62952 (published as WO/2010/051527),and PCT/US09/69390, all of which are herein incorporated by reference intheir entireties for all purposes. Additional pathways have beendescribed for the synthesis of 1-butanol (See, e.g., commonly owned U.S.Provisional Application Nos. 60/940,877 and 60/945,576, as well asWO/2010/017230 and WO/2010/031772), 2-butanol (See, e.g.,WO/2007/130518, WO/2007/130521, and WO/2009/134276), 2-butanone (See,e.g., WO/2007/130518, WO/2007/130521, and WO/2009/134276),2,3-butanediol (See, e.g., WO/2007/130518, WO/2007/130521, andWO/2009/134276), valine (See, e.g., WO/2001/021772, and McCourt et al.,2006, Amino Acids 31: 173-210), leucine (See, e.g., WO/2001/021772, andMcCourt et al., 2006, Amino Acids 31: 173-210), pantothenic acid (See,e.g., WO/2001/021772), and 3-methyl-1-butanol (See, e.g.,WO/2008/098227, Atsumi et al., 2008, Nature 451: 86-89, and Connor etal., 2008, Appl. Environ. Microbiol. 74: 5769-5775). Each of thesepathways shares the common intermediate acetolactate. Therefore, theproduct yield from these biosynthetic pathways will in part depend uponthe amount of acetolactate that is available to downstream enzymes ofsaid biosynthetic pathways.

In various embodiments described herein, the present invention providesrecombinant microorganisms that comprise an isobutanol producingmetabolic pathway. Recombinant microorganisms provided herein canexpress a plurality of heterologous and/or native target enzymesinvolved in pathways for the production isobutanol from a suitablecarbon source.

Accordingly, metabolically “engineered” or “modified” microorganisms areproduced via the introduction of genetic material into a host orparental microorganism of choice and/or by modification of theexpression of native genes, thereby modifying or altering the cellularphysiology and biochemistry of the microorganism. Through theintroduction of genetic material and/or the modification of theexpression of native genes the parental microorganism acquires newproperties, e.g. the ability to produce a new, or greater quantities of,an intracellular metabolite. As described herein, the introduction ofgenetic material into and/or the modification of the expression ofnative genes in a parental microorganism results in a new or modifiedability to produce isobutanol. The genetic material introduced intoand/or the genes modified for expression in the parental microorganismcontains gene(s), or parts of genes, coding for one or more of theenzymes involved in a biosynthetic pathway for the production ofisobutanol and may also include additional elements for the expressionand/or regulation of expression of these genes, e.g. promoter sequences.

In addition to the introduction of a genetic material into a host orparental microorganism, an engineered or modified microorganism can alsoinclude alteration, disruption, deletion or knocking-out of a gene orpolynucleotide to alter the cellular physiology and biochemistry of themicroorganism. Through the alteration, disruption, deletion orknocking-out of a gene or polynucleotide the microorganism acquires newor improved properties (e.g., the ability to produce a new metabolite orgreater quantities of an intracellular metabolite, improve the flux of ametabolite down a desired pathway, and/or reduce the production ofbyproducts).

Recombinant microorganisms provided herein may also produce metabolitesin quantities not available in the parental microorganism. A“metabolite” refers to any substance produced by metabolism or asubstance necessary for or taking part in a particular metabolicprocess. A metabolite can be an organic compound that is a startingmaterial (e.g., glucose or pyruvate), an intermediate (e.g.,2-ketoisovalerate), or an end product (e.g., isobutanol) of metabolism.Metabolites can be used to construct more complex molecules, or they canbe broken down into simpler ones. Intermediate metabolites may besynthesized from other metabolites, perhaps used to make more complexsubstances, or broken down into simpler compounds, often with therelease of chemical energy.

Exemplary metabolites include glucose, pyruvate, and isobutanol. Themetabolite isobutanol can be produced by a recombinant microorganismmetabolically engineered to express or over-express a metabolic pathwaythat converts pyruvate to isobutanol. An exemplary metabolic pathwaythat converts pyruvate to isobutanol may be comprised of an acetohydroxyacid synthase (ALS), a ketolacid reductoisomerase (KARI), adihyroxy-acid dehydratase (DHAD), a 2-keto-acid decarboxylase (KIVD),and an alcohol dehydrogenase (ADH). Exemplary metabolic pathways thatconvert pyruvate to isobutanol are disclosed in WO/2007/050671,WO/2008/098227, and Atsumi et al., Nature, 2008 Jan. 3; 451(7174):86-9.

Accordingly, provided herein are recombinant microorganisms that produceisobutanol and in some aspects may include the elevated expression oftarget enzymes such as ALS, KARI, DHAD, KIVD, and ADH.

The disclosure identifies specific genes useful in the methods,compositions and organisms of the disclosure; however it will berecognized that absolute identity to such genes is not necessary. Forexample, changes in a particular gene or polynucleotide comprising asequence encoding a polypeptide or enzyme can be performed and screenedfor activity. Typically such changes comprise conservative mutation andsilent mutations. Such modified or mutated polynucleotides andpolypeptides can be screened for expression of a functional enzyme usingmethods known in the art.

Due to the inherent degeneracy of the genetic code, otherpolynucleotides which encode substantially the same or functionallyequivalent polypeptides can also be used to clone and express thepolynucleotides encoding such enzymes.

As will be understood by those of skill in the art, it can beadvantageous to modify a coding sequence to enhance its expression in aparticular host. The genetic code is redundant with 64 possible codons,but most organisms typically use a subset of these codons. The codonsthat are utilized most often in a species are called optimal codons, andthose not utilized very often are classified as rare or low-usagecodons. Codons can be substituted to reflect the preferred codon usageof the host, a process sometimes called “codon optimization” or“controlling for species codon bias.”

Optimized coding sequences containing codons preferred by a particularprokaryotic or eukaryotic host (see also, Murray et al. (1989) Nucl.Acids Res. 17:477-508) can be prepared, for example, to increase therate of translation or to produce recombinant RNA transcripts havingdesirable properties, such as a longer half-life, as compared withtranscripts produced from a non-optimized sequence. Translation stopcodons can also be modified to reflect host preference. For example,typical stop codons for S. cerevisiae and mammals are UAA and UGA,respectively. The typical stop codon for monocotyledonous plants is UGA,whereas insects and E. coli commonly use UAA as the stop codon (Dalphinet al. (1996) Nucl. Acids Res. 24: 216-218). Methodology for optimizinga nucleotide sequence for expression in a plant is provided, forexample, in U.S. Pat. No. 6,015,891, and the references cited therein.

Those of skill in the art will recognize that, due to the degeneratenature of the genetic code, a variety of DNA compounds differing intheir nucleotide sequences can be used to encode a given enzyme of thedisclosure. The native DNA sequence encoding the biosynthetic enzymesdescribed above are referenced herein merely to illustrate an embodimentof the disclosure, and the disclosure includes DNA compounds of anysequence that encode the amino acid sequences of the polypeptides andproteins of the enzymes utilized in the methods of the disclosure. Insimilar fashion, a polypeptide can typically tolerate one or more aminoacid substitutions, deletions, and insertions in its amino acid sequencewithout loss or significant loss of a desired activity. The disclosureincludes such polypeptides with different amino acid sequences than thespecific proteins described herein so long as they modified or variantpolypeptides have the enzymatic anabolic or catabolic activity of thereference polypeptide. Furthermore, the amino acid sequences encoded bythe DNA sequences shown herein merely illustrate embodiments of thedisclosure.

In addition, homologs of enzymes useful for generating metabolites areencompassed by the microorganisms and methods provided herein.

As used herein, two proteins (or a region of the proteins) aresubstantially homologous when the amino acid sequences have at leastabout 30%, 40%, 50% 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% identity. To determine the percentidentity of two amino acid sequences, or of two nucleic acid sequences,the sequences are aligned for optimal comparison purposes (e.g., gapscan be introduced in one or both of a first and a second amino acid ornucleic acid sequence for optimal alignment and non-homologous sequencescan be disregarded for comparison purposes). In one embodiment, thelength of a reference sequence aligned for comparison purposes is atleast 30%, typically at least 40%, more typically at least 50%, evenmore typically at least 60%, and even more typically at least 70%, 80%,90%, 100% of the length of the reference sequence. The amino acidresidues or nucleotides at corresponding amino acid positions ornucleotide positions are then compared. When a position in the firstsequence is occupied by the same amino acid residue or nucleotide as thecorresponding position in the second sequence, then the molecules areidentical at that position (as used herein amino acid or nucleic acid“identity” is equivalent to amino acid or nucleic acid “homology”). Thepercent identity between the two sequences is a function of the numberof identical positions shared by the sequences, taking into account thenumber of gaps, and the length of each gap, which need to be introducedfor optimal alignment of the two sequences.

When “homologous” is used in reference to proteins or peptides, it isrecognized that residue positions that are not identical often differ byconservative amino acid substitutions. A “conservative amino acidsubstitution” is one in which an amino acid residue is substituted byanother amino acid residue having a side chain (R group) with similarchemical properties (e.g., charge or hydrophobicity). In general, aconservative amino acid substitution will not substantially change thefunctional properties of a protein. In cases where two or more aminoacid sequences differ from each other by conservative substitutions, thepercent sequence identity or degree of homology may be adjusted upwardsto correct for the conservative nature of the substitution. Means formaking this adjustment are well known to those of skill in the art (see,e.g., Pearson W. R. Using the FASTA program to search protein and DNAsequence databases, Methods in Molecular Biology,1994, 25:365-89, herebyincorporated herein by reference).

The following six groups each contain amino acids that are conservativesubstitutions for one another: 1) Serine (S), Threonine (T); 2) AsparticAcid (D), Glutamic Acid (E); 3) Asparagine (N), Glutamine (Q); 4)Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine(M), Alanine (A), Valine (V), and 6) Phenylalanine (F), Tyrosine (Y),Tryptophan (W).

Sequence homology for polypeptides, which is also referred to as percentsequence identity, is typically measured using sequence analysissoftware. See, e.g., the Sequence Analysis Software Package of theGenetics Computer Group (GCG), University of Wisconsin BiotechnologyCenter, 910 University Avenue, Madison, Wis. 53705. Protein analysissoftware matches similar sequences using measure of homology assigned tovarious substitutions, deletions and other modifications, includingconservative amino acid substitutions. For instance, GCG containsprograms such as “Gap” and “Bestfit” which can be used with defaultparameters to determine sequence homology or sequence identity betweenclosely related polypeptides, such as homologous polypeptides fromdifferent species of organisms or between a wild type protein and amutant protein thereof. See, e.g., GCG Version 6.1.

A typical algorithm used comparing a molecule sequence to a databasecontaining a large number of sequences from different organisms is thecomputer program BLAST (Altschul, S. F., et al. (1990) “Basic localalignment search tool.” J. Mol. Biol. 215:403-410; Gish, W. and States,D. J. (1993) “Identification of protein coding regions by databasesimilarity search.” Nature Genet. 3:266-272; Madden, T. L., et al.(1996) “Applications of network BLAST server” Meth. Enzymol.266:131-141; Altschul, S. F., et al. (1997) “Gapped BLAST and PSI-BLAST:a new generation of protein database search programs.” Nucleic AcidsRes. 25:3389-3402; Zhang, J. and Madden, T. L. (1997) “PowerBLAST: A newnetwork BLAST application for interactive or automated sequence analysisand annotation.” Genome Res. 7:649-656), especially blastp or tblastn(Altschul, S. F., et al. (1997) “Gapped BLAST and PSI-BLAST: a newgeneration of protein database search programs.” Nucleic Acids Res.25:3389-3402). Typical parameters for BLASTp are: Expectation value: 10(default); Filter: seg (default); Cost to open a gap: 11 (default); Costto extend a gap: 1 (default); Max. alignments: 100 (default); Word size:11 (default); No. of descriptions: 100 (default); Penalty Matrix:BLOWSUM62.

When searching a database containing sequences from a large number ofdifferent organisms, it is typical to compare amino acid sequences.Database searching using amino acid sequences can be measured byalgorithms other than blastp known in the art. For instance, polypeptidesequences can be compared using FASTA, a program in GCG Version 6.1.FASTA provides alignments and percent sequence identity of the regionsof the best overlap between the query and search sequences (Pearson, W.R. (1990) “Rapid and Sensitive Sequence Comparison with FASTP and FASTA”Meth. Enzymol. 183:63-98). For example, a percent sequence identitybetween amino acid sequences can be determined using FASTA with itsdefault parameters (a word size of 2 and the PAM250 scoring matrix), asprovided in GCG Version 6.1, hereby incorporated herein by reference.

The disclosure provides metabolically engineered microorganismscomprising a biochemical pathway for the production of isobutanol from asuitable substrate at a high yield. A metabolically engineeredmicroorganism of the disclosure comprises one or more recombinantpolynucleotides within the genome of the organism or external to thegenome within the organism. The microorganism can comprise a reduction,disruption or knockout of a gene found in the wild-type organism and/orintroduction of a heterologous polynucleotide and/or expression oroverexpression of an endogenous polynucleotide.

In one aspect, the disclosure provides a recombinant microorganismcomprising elevated expression of at least one target enzyme as comparedto a parental microorganism or encodes an enzyme not found in theparental organism. In another or further aspect, the microorganismcomprises a reduction, disruption or knockout of at least one geneencoding an enzyme that competes with a metabolite necessary for theproduction of isobutanol. The recombinant microorganism produces atleast one metabolite involved in a biosynthetic pathway for theproduction of isobutanol. In general, the recombinant microorganismscomprises at least one recombinant metabolic pathway that comprises atarget enzyme and may further include a reduction in activity orexpression of an enzyme in a competitive biosynthetic pathway. Thepathway acts to modify a substrate or metabolic intermediate in theproduction of isobutanol. The target enzyme is encoded by, and expressedfrom, a polynucleotide derived from a suitable biological source. Insome embodiments, the polynucleotide comprises a gene derived from aprokaryotic or eukaryotic source and recombinantly engineered into themicroorganism of the disclosure. In other embodiments, thepolynucleotide comprises a gene that is native to the host organism.

It is understood that a range of microorganisms can be modified toinclude a recombinant metabolic pathway suitable for the production ofisobutanol. In various embodiments, microorganisms may be selected fromyeast microorganisms. Yeast microorganisms for the production ofisobutanol may be selected based on certain characteristics:

One characteristic may include the property that the microorganism isselected to convert various carbon sources into isobutanol. The term“carbon source” generally refers to a substance suitable to be used as asource of carbon for prokaryotic or eukaryotic cell growth. Carbonsources include, but are not limited to, biomass hydrolysates, starch,sucrose, cellulose, hemicellulose, xylose, and lignin, as well asmonomeric components of these substrates. Carbon sources can comprisevarious organic compounds in various forms, including, but not limitedto polymers, carbohydrates, acids, alcohols, aldehydes, ketones, aminoacids, peptides, etc. These include, for example, variousmonosaccharides such as glucose, dextrose (D-glucose), maltose,oligosaccharides, polysaccharides, saturated or unsaturated fatty acids,succinate, lactate, acetate, ethanol, etc., or mixtures thereof.Photosynthetic organisms can additionally produce a carbon source as aproduct of photosynthesis. In some embodiments, carbon sources may beselected from biomass hydrolysates and glucose. The term “biomass” asused herein refers primarily to the stems, leaves, and starch-containingportions of green plants, and is mainly comprised of starch, lignin,cellulose, hemicellulose, and/or pectin. Biomass can be decomposed byeither chemical or enzymatic treatment to the monomeric sugars andphenols of which it is composed (Wyman, C. E. 2003 BiotechnologicalProgress 19:254-62). This resulting material, called biomasshydrolysate, is neutralized and treated to remove trace amounts oforganic material that may adversely affect the biocatalyst, and is thenused as a feed stock for fermentations using a biocatalyst.

Accordingly, in one embodiment, the recombinant microorganism hereindisclosed can convert a variety of carbon sources to products, includingbut not limited to glucose, galactose, mannose, xylose, arabinose,lactose, sucrose, and mixtures thereof.

The recombinant microorganism may thus further include a pathway for thefermentation of isobutanol from five-carbon (pentose) sugars includingxylose. Most yeast species metabolize xylose via a complex route, inwhich xylose is first reduced to xylitol via a xylose reductase (XR)enzyme. The xylitol is then oxidized to xylulose via a xylitoldehydrogenase (XDH) enzyme. The xylulose is then phosphorylated via axylulokinase (XK) enzyme. This pathway operates inefficiently in yeastspecies because it introduces a redox imbalance in the cell. Thexylose-to-xylitol step uses NADH as a cofactor, whereas thexylitol-to-xylulose step uses NADPH as a cofactor. Other processes mustoperate to restore the redox imbalance within the cell. This often meansthat the organism cannot grow anaerobically on xylose or other pentosesugar. Accordingly, a yeast species that can efficiently ferment xyloseand other pentose sugars into a desired fermentation product istherefore very desirable.

Thus, in one embodiment, the recombinant is engineered to express afunctional exogenous xylose isomerase. Exogenous xylose isomerasesfunctional in yeast are known in the art. See, e.g., Rajgarhia et al,US20060234364, which is herein incorporated by reference in itsentirety. In another embodiment, the exogenous xylose isomerase gene isoperatively linked to promoter and terminator sequences that arefunctional in the yeast cell.

In another embodiment, the recombinant microorganism has a deletion ordisruption of a native gene that encodes for an enzyme (e.g. XR and/orXDH) that catalyzes the conversion of xylose to xylitol. Thus, in oneembodiment, the recombinant microorganism is engineered to exhibitreduced xylose reductase (XR) activity. In another embodiment, therecombinant microorganism is engineered to exhibit reduced xylitoldehydrogenase (XDH) activity. In yet another embodiment, the recombinantmicroorganism also contains a functional, exogenous xylulokinase (XK)gene operatively linked to promoter and terminator sequences that arefunctional in the yeast cell. In one embodiment, the xylulokinase (XK)gene is overexpressed.

In one embodiment, the microorganism has reduced or no pyruvatedecarboxylase (PDC) activity. PDC catalyzes the decarboxylation ofpyruvate to acetaldehyde, which is then reduced to ethanol by ADH via anoxidation of NADH to NAD+. Ethanol production is the main pathway tooxidize the NADH from glycolysis. Deletion of this pathway increases thepyruvate and the reducing equivalents (NADH) available for theisobutanol pathway. Accordingly, deletion of PDC genes further increasesthe yield of isobutanol.

In another embodiment, the microorganism has reduced or noglycerol-3-phosphate dehydrogenase (GPD) activity. GPD catalyzes thereduction of dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate(G3P) via the oxidation of NADH to NAD+. Glycerol is then produced fromG3P by Glycerol-3-phosphatase (GPP). Glycerol production is a secondarypathway to oxidize excess NADH from glycolysis. Reduction or eliminationof this pathway increases the pyruvate and reducing equivalents (NADH)available for the isobutanol pathway. Thus, deletion of GPD genesfurther increases the yield of isobutanol.

In yet another embodiment, the microorganism has reduced or no PDCactivity and reduced or no GPD activity.

Another characteristic may include the property that the wild-type orparental microorganism is non-fermenting. In other words, it cannotmetabolize a carbon source anaerobically while the yeast is able tometabolize a carbon source in the presence of oxygen. Non-fermentingyeast refers to both naturally occurring yeasts as well as geneticallymodified yeast. During anaerobic fermentation with fermentative yeast,the main pathway to oxidize the NADH from glycolysis is through theproduction of ethanol. Ethanol is produced by alcohol dehydrogenase(ADH) via the reduction of acetaldehyde, which is generated frompyruvate by pyruvate decarboxylase (PDC). Thus, in one embodiment, afermentative yeast can be engineered to be non-fermentative by thereduction or elimination of the native PDC activity. Thus, most of thepyruvate produced by glycolysis is not consumed by PDC and is availablefor the isobutanol pathway. Deletion of this pathway increases thepyruvate and the reducing equivalents available for the isobutanolpathway. Fermentative pathways contribute to low yield and lowproductivity of isobutanol. Accordingly, deletion of PDC may increaseyield and productivity of isobutanol.

A third characteristic may include the property that the biocatalyst isselected to convert various carbon sources into isobutanol.

In one embodiment, the yeast microorganisms may be selected from the“Saccharomyces Yeast Clade”, defined as an ascomycetous yeast taxonomicclass by Kurtzman and Robnett in 1998 (“Identification and phylogeny ofascomycetous yeast from analysis of nuclear large subunit (26S)ribosomal DNA partial sequences.” Antonie van Leeuwenhoek 73: 331-371,See FIG. 2 of Leeuwenhoek reference). They were able to determine therelatedness of approximately 500 yeast species by comparing thenucleotide sequence of the D1/D2 domain at the 5′ end of the geneencoding the large ribosomal subunit 26S. In pair-wise comparisons ofthe D1/D2 nucleotide sequences of S. cerevisiae and the two most distantyeast from S. cerevisiae, K. lactis and K. marxianus, share greater than80% identity.

The term “Saccharomyces sensu stricto” taxonomy group is a cluster ofyeast species that are highly related to S. cerevisiae (Rainieri, S. etal 2003. Saccharomyces Sensu Stricto: Systematics, Genetic Diversity andEvolution. J. Biosci Bioengin 96(1)1-9. Saccharomyces sensu strictoyeast species include but are not limited to S. cerevisiae, S.cerevisiae, S. kudriavzevii, S. mikatae, S. bayanus, S. uvarum, S.carocanis and hybrids derived from these species (Masneuf et al. 1998.New Hybrids between Saccharomyces Sensu Stricto Yeast Species FoundAmong Wine and Cider Production Strains. Yeast 7(1)61-72).

An ancient whole genome duplication (WGD) event occurred during theevolution of the hemiascomycete yeast and was discovered usingcomparative genomic tools (Kellis et al 2004 “Proof and evolutionaryanalysis of ancient genome duplication in the yeast S. cerevisiae.”Nature 428:617-624. Dujon et al 2004 “Genome evolution in yeasts.”Nature 430:35-44. Langkjaer et al 2003 “Yeast genome duplication wasfollowed by asynchronous differentiation of duplicated genes.” Nature428:848-852. Wolfe and Shields 1997 “Molecular evidence for an ancientduplication of the entire yeast genome.” Nature 387:708-713.) Using thismajor evolutionary event, yeast can be divided into species thatdiverged from a common ancestor following the WGD event (termed“post-WGD yeast” herein) and species that diverged from the yeastlineage prior to the WGD event (termed “pre-WGD yeast” herein).

Accordingly, in one embodiment, the yeast microorganism may be selectedfrom a post-WGD yeast genus, including but not limited to Saccharomycesand Candida. The favored post-WGD yeast species include: S. cerevisiae,S. uvarum, S. bayanus, S. paradoxus, S. casteffi, and C. glabrata.

In another embodiment, the yeast microorganism may be selected from apre-whole genome duplication (pre-WGD) yeast genus including but notlimited to Saccharomyces, Kluyveromyces, Candida, Pichia, Issatchenkia,Debaryomyces, Hansenula, Yarrowia and, Schizosaccharomyces.Representative pre-WGD yeast species include: S. kluyveri, K.thermotolerans, K. marxianus, K. waltii, K. lactis, C. tropicalis, P.pastoris, P. anomala, P. stipitis, I. orientalis, I. occidentalis, I.scutulata, D. hansenii, H. anomala, Y. lipolytica, and S. pombe.

A yeast microorganism may be either Crabtree-negative orCrabtree-positive. A yeast cell having a Crabtree-negative phenotype isany yeast cell that does not exhibit the Crabtree effect. The term“Crabtree-negative” refers to both naturally occurring and geneticallymodified organisms. Briefly, the Crabtree effect is defined as theinhibition of oxygen consumption by a microorganism when cultured underaerobic conditions due to the presence of a high concentration ofglucose (e.g., 50 g-glucose L⁻¹). In other words, a yeast cell having aCrabtree-positive phenotype continues to ferment irrespective of oxygenavailability due to the presence of glucose, while a yeast cell having aCrabtree-negative phenotype does not exhibit glucose mediated inhibitionof oxygen consumption.

Accordingly, in one embodiment the yeast microorganism may be selectedfrom yeast with a Crabtree-negative phenotype including but not limitedto the following genera: Kluyveromyces, Pichia, Issatchenkia, Hansenula,and Candida. Crabtree-negative species include but are not limited to:K. lactis, K. marxianus, P. anomala, P. stipitis, I. orientalis, I.occidentalis, I. scutulata, H. anomala, and C. utilis.

In another embodiment, the yeast microorganism may be selected from ayeast with a Crabtree-positive phenotype, including but not limited toSaccharomyces, Kluyveromyces, Zygosaccharomyces, Debaryomyces, Pichiaand Schizosaccharomyces. Crabtree-positive yeast species include but arenot limited to: S. cerevisiae, S. uvarum, S. bayanus, S. paradoxus, S.casteffi, S. kluyveri, K. thermotolerans, C. glabrata, Z. bailli, Z.rouxii, D. hansenii, P. pastorius, and S. pombe.

In some embodiments, the recombinant microorganisms may bemicroorganisms that are non-fermenting yeast microorganisms, including,but not limited to those, classified into a genera selected from thegroup consisting of Tricosporon, Rhodotorula, or Myxozyma.

In one embodiment, a yeast microorganism is engineered to convert acarbon source, such as glucose, to pyruvate by glycolysis and thepyruvate is converted to isobutanol via an engineered isobutanol pathway(See, e.g., WO/2007/050671, WO/2008/098227, and Atsumi et al., Nature,2008 Jan. 3; 451(7174):86-9). Alternative pathways for the production ofisobutanol have been described in WO/2007/050671 and in Dickinson etal., Journal of Biological Chemistry 273:25751-15756 (1998).

Accordingly, in one embodiment, the engineered isobutanol pathway toconvert pyruvate to isobutanol can be comprised of the followingreactions:

-   1. 2 pyruvate→acetolactate+CO₂-   2. acetolactate+NAD(P)H→2,3-dihydroxyisovalerate+NAD(P)⁺-   3. 2,3-dihydroxyisovalerate→alpha-ketoisovalerate-   4. alpha-ketoisovalerate→isobutyraldehyde+CO₂-   5. isobutyraldehyde+NAD(P)H→isobutanol+NAD(P)⁺

These reactions are carried out by the enzymes 1) Acetolactate Synthase(ALS), 2) Keto-acid Reducto-Isomerase (KARI), 3) Dihydroxy-aciddehydratase (DHAD), 4) Keto-isovalerate decarboxylase (KIVD), and 5) anAlcohol dehydrogenase (ADH).

In another embodiment, the yeast microorganism is engineered tooverexpress these enzymes. For example, these enzymes can be encoded bynative genes. Alternatively, these enzymes can be encoded byheterologous genes. For example, ALS can be encoded by the aisS gene ofB. subtilis, alsS of L. lactis, or the ilvK gene of K. pneumonia. Forexample, KARI can be encoded by the ilvC genes of E. coli, C.glutamicum, M. maripaludis, or Piromyces sp E2. For example, DHAD can beencoded by the ilvD genes of E. coli, C. glutamicum, or L. lactis. KIVDcan be encoded by the kivD gene of L. lactis. ADH can be encoded byADH2, ADH6, or ADH7 of S. cerevisiae.

In one embodiment, pathway steps 2 and 5 may be carried out by KARI andADH enzymes that utilize NADH (rather than NADPH) as a co-factor. Suchenzymes are described in commonly owned and co-pending applications U.S.Ser. No. 12/610,784 and PCT/US09/62952 (published as WO/2010/051527),which are herein incorporated by reference in their entireties for allpurposes. The present inventors have found that utilization ofNADH-dependent KARI and ADH enzymes to catalyze pathway steps 2 and 5,respectively, surprisingly enables production of isobutanol underanaerobic conditions. Thus, in one embodiment, the recombinantmicroorganisms of the present invention may use an NADH-dependent KARIto catalyze the conversion of acetolactate (+NADH) to produce 2,3-dihydroxyisovalerate. In another embodiment, the recombinantmicroorganisms of the present invention may use an NADH-dependent ADH tocatalyze the conversion of isobutyraldehyde (+NADH) to produceisobutanol. In yet another embodiment, the recombinant microorganisms ofthe present invention may use both an NADH-dependent KARI to catalyzethe conversion of acetolactate (+NADH) to produce 2,3-dihydroxyisovalerate, and an NADH-dependent ADH to catalyze theconversion of isobutyraldehyde (+NADH) to produce isobutanol.

The yeast microorganism of the invention may be engineered to haveincreased ability to convert pyruvate to isobutanol. In one embodiment,the yeast microorganism may be engineered to have increased ability toconvert pyruvate to isobutyraldehyde. In another embodiment, the yeastmicroorganism may be engineered to have increased ability to convertpyruvate to keto-isovalerate. In another embodiment, the yeastmicroorganism may be engineered to have increased ability to convertpyruvate to 2, 3-dihydroxyisovalerate. In another embodiment, the yeastmicroorganism may be engineered to have increased ability to convertpyruvate to acetolactate.

Furthermore, any of the genes encoding the foregoing enzymes (or anyothers mentioned herein (or any of the regulatory elements that controlor modulate expression thereof)) may be optimized by genetic/proteinengineering techniques, such as directed evolution or rationalmutagenesis, which are known to those of ordinary skill in the art. Suchaction allows those of ordinary skill in the art to optimize the enzymesfor expression and activity in yeast.

In addition, genes encoding these enzymes can be identified from otherfungal and bacterial species and can be expressed for the modulation ofthis pathway. A variety of organisms could serve as sources for theseenzymes, including, but not limited to, Saccharomyces spp., including S.cerevisiae and S. uvarum, Kluyveromyces spp., including K.thermotolerans, K. lactis, and K. marxianus, Pichia spp., Hansenulaspp., including H. polymorpha, Candida spp., Trichosporon spp.,Yamadazyma spp., including Y. stipitis, Torulaspora spp, including T.pretoriensis, Schizosaccharomyces spp., including S. pombe, Cryptococcusspp., Aspergillus spp., Neurospora spp., or Ustilago spp. Sources ofgenes from anaerobic fungi include, but not limited to, Piromyces spp.,Orpinomyces spp., or Neocallimastix spp. Sources of prokaryotic enzymesthat are useful include, but not limited to, Escherichia coli, Zymomonasmobilis, Staphylococcus aureus, Bacillus spp., Clostridium spp.,Corynebacterium spp., Pseudomonas spp., Lactococcus spp., Enterobacterspp., and Salmonella spp.

Methods in General Identification of PDC in a Yeast Microorganism

Any method can be used to identify genes that encode for enzymes withpyruvate decarboxylase (PDC) activity. PDC catalyzes the decarboxylationof pyruvate to form acetaldehyde. Generally, homologous or similar PDCgenes and/or homologous or similar PDC enzymes can be identified byfunctional, structural, and/or genetic analysis. In most cases,homologous or similar PDC genes and/or homologous or similar PDC enzymeswill have functional, structural, or genetic similarities. Techniquesknown to those skilled in the art may be suitable to identify homologousgenes and homologous enzymes. Generally, analogous genes and/oranalogous enzymes can be identified by functional analysis and will havefunctional similarities. Techniques known to those skilled in the artmay be suitable to identify analogous genes and analogous enzymes. Forexample, to identify homologous or analogous genes, proteins, orenzymes, techniques may include, but not limited to, cloning a PDC geneby PCR using primers based on a published sequence of a gene/enzyme orby degenerate PCR using degenerate primers designed to amplify aconserved region among PDC genes. Further, one skilled in the art canuse techniques to identify homologous or analogous genes, proteins, orenzymes with functional homology or similarity. Techniques includeexamining a cell or cell culture for the catalytic activity of an enzymethrough in vitro enzyme assays for said activity, then isolating theenzyme with said activity through purification, determining the proteinsequence of the enzyme through techniques such as Edman degradation,design of PCR primers to the likely nucleic acid sequence, amplificationof said DNA sequence through PCR, and cloning of said nucleic acidsequence. To identify homologous or similar genes and/or homologous orsimilar enzymes, analogous genes and/or analogous enzymes or proteins,techniques also include comparison of data concerning a candidate geneor enzyme with databases such as BRENDA, KEGG, or MetaCYC. The candidategene or enzyme may be identified within the above mentioned databases inaccordance with the teachings herein. Furthermore, PDC activity can bedetermined phenotypically. For example, ethanol production underfermentative conditions can be assessed. A lack of ethanol productionmay be indicative of a yeast microorganism with no PDC activity.Examples of yeast pyruvate decarboxylase genes that may be targeted fordisruption may be found in U.S. Pat. No. 7,326,550. Target genes fordisruption include, but are not limited, to PDC1 (GenBank Accession No.CAA97573.1), PDC5 (GenBank Accession No. CAA97705.1), and PDC6 (GenBankAccession No. CAA97089.1) from S. cerevisiae, as well as genes encodingpyruvate decarboxylases from K. lactis (GenBank Accession No.CAA59953.1), K. marxianus (AAA35267.1), P. stipitis (GenBank AccessionNo. AACO3164.3), C. glabrata (AAN77243.1), S. pombe (GenBank AccessionNo. NP_(—)592796.2), and Y. lipolytica (CAG80835.1). Other target genes,such as those encoding pyruvate decarboxylase proteins having at leastabout 50-55%, 55%-60%, 60-65%, 65%-70%, 75-80%, 80-85%, 85% -90%,90%-95%, or at least about 98% sequence identity to the S. cerevisiaepyruvate decarboxylases may be identified in the literature and inbioinformatics databases well known to the skilled person.

Identification of GPD in a Yeast Microorganism

Any method can be used to identify genes that encode for enzymes withglycerol-3-phosphate dehydrogenase (GPD) activity. GPD catalyzes thereduction of dihydroxyacetone phosphate (DHAP) to glycerol-3-phosphate(G3P) with the corresponding oxidation of NADH to NAD+. Generally,homologous or similar GPD genes and/or homologous or similar GPD enzymescan be identified by functional, structural, and/or genetic analysis. Inmost cases, homologous or similar GPD genes and/or homologous or similarGPD enzymes will have functional, structural, or genetic similarities.Techniques known to those skilled in the art may be suitable to identifyhomologous genes and homologous enzymes. Generally, analogous genesand/or analogous enzymes can be identified by functional analysis andwill have functional similarities. Techniques known to those skilled inthe art may be suitable to identify analogous genes and analogousenzymes. For example, to identify homologous or analogous genes,proteins, or enzymes, techniques may include, but not limited to,cloning a GPD gene by PCR using primers based on a published sequence ofa gene/enzyme or by degenerate PCR using degenerate primers designed toamplify a conserved region among GPD genes. Further, one skilled in theart can use techniques to identify homologous or analogous genes,proteins, or enzymes with functional homology or similarity. Techniquesinclude examining a cell or cell culture for the catalytic activity ofan enzyme through in vitro enzyme assays for said activity, thenisolating the enzyme with said activity through purification,determining the protein sequence of the enzyme through techniques suchas Edman degradation, design of PCR primers to the likely nucleic acidsequence, amplification of said DNA sequence through PCR, and cloning ofsaid nucleic acid sequence. To identify homologous or similar genesand/or homologous or similar enzymes, analogous genes and/or analogousenzymes or proteins, techniques also include comparison of dataconcerning a candidate gene or enzyme with databases such as BRENDA,KEGG, or MetaCYC. The candidate gene or enzyme may be identified withinthe above mentioned databases in accordance with the teachings herein.Furthermore, GPD activity can be determined phenotypically. For example,glycerol production under fermentative conditions can be assessed. Alack of glycerol production may be indicative of a yeast microorganismwith no GPD activity. Examples of yeast glycerol-3-phosphatedehydrogenase genes that may be targeted for disruption may be found inUS 2009/0053782. Other target genes, such as those encodingglycerol-3-phosphate dehydrogenase proteins having at least about50-55%, 55%-60%, 60-65%, 65%-70%, 75-80%, 80-85%, 85%-90%, 90%-95%, orat least about 98% sequence identity to the S. cerevisiaeglycerol-3-phosphate dehydrogenases may be identified in the literatureand in bioinformatics databases well known to the skilled person.

Genetic Insertions and Deletions

Any method can be used to introduce a nucleic acid molecule into yeastand many such methods are well known. For example, transformation andelectroporation are common methods for introducing nucleic acid intoyeast cells. See, e.g., Gietz et al., Nucleic Acids Res. 27:69-74(1992); Ito et al., J. Bacteriol. 153:163-168 (1983); and Becker andGuarente, Methods in Enzymology 194:182-187 (1991).

In an embodiment, the integration of a gene of interest into a DNAfragment or target gene of a yeast microorganism occurs according to theprinciple of homologous recombination. According to this embodiment, anintegration cassette containing a module comprising at least one yeastmarker gene and/or the gene to be integrated (internal module) isflanked on either side by DNA fragments homologous to those of the endsof the targeted integration site (recombinogenic sequences). Aftertransforming the yeast with the cassette by appropriate methods, ahomologous recombination between the recombinogenic sequences may resultin the internal module replacing the chromosomal region in between thetwo sites of the genome corresponding to the recombinogenic sequences ofthe integration cassette. (Orr-Weaver et al., Proc Natl Acad Sci USA78:6354-6358 (1981))

In an embodiment, the integration cassette for integration of a gene ofinterest into a yeast microorganism includes the heterologous gene underthe control of an appropriate promoter and terminator together with theselectable marker flanked by recombinogenic sequences for integration ofa heterologous gene into the yeast chromosome. In an embodiment, theheterologous gene includes an appropriate native gene desired toincrease the copy number of a native gene(s). The selectable marker genecan be any marker gene used in yeast, including but not limited to,HIS3, TRP1, LEU2, URA3, bar, ble, hph, and kan. The recombinogenicsequences can be chosen at will, depending on the desired integrationsite suitable for the desired application.

In another embodiment, integration of a gene into the chromosome of theyeast microorganism may occur via random integration (Kooistra, R.,Hooykaas, P. J. J., Steensma, H. Y. 2004. Yeast 21: 781-792).

Additionally, in an embodiment, certain introduced marker genes areremoved from the genome using techniques well known to those skilled inthe art. For example, URA3 marker loss can be obtained by plating URA3containing cells in FOA (5-fluoro-orotic acid) containing medium andselecting for FOA resistant colonies (Boeke, J. et al, 1984, Mol. Gen.Genet, 197, 345-47).

The exogenous nucleic acid molecule contained within a yeast cell of thedisclosure can be maintained within that cell in any form. For example,exogenous nucleic acid molecules can be integrated into the genome ofthe cell or maintained in an episomal state that can stably be passed on(“inherited”) to daughter cells. Such extra-chromosomal genetic elements(such as plasmids, etc.) can additionally contain selection markers thatensure the presence of such genetic elements in daughter cells.Moreover, the yeast cells can be stably or transiently transformed. Inaddition, the yeast cells described herein can contain a single copy, ormultiple copies of a particular exogenous nucleic acid molecule asdescribed above.

Reduction of Enzymatic Activity

Yeast microorganisms within the scope of the invention may have reducedenzymatic activity such as reduced pyruvate decarboxylase activity. Theterm “reduced” as used herein with respect to a particular enzymaticactivity refers to a lower level of enzymatic activity than thatmeasured in a comparable yeast cell of the same species. The termreduced also refers to the elimination of enzymatic activity than thatmeasured in a comparable yeast cell of the same species. Thus, yeastcells lacking pyruvate decarboxylase activity are considered to havereduced pyruvate decarboxylase activity since most, if not all,comparable yeast strains have at least some pyruvate decarboxylaseactivity. Such reduced enzymatic activities can be the result of lowerenzyme concentration, lower specific activity of an enzyme, or acombination thereof. Many different methods can be used to make yeasthaving reduced enzymatic activity. For example, a yeast cell can beengineered to have a disrupted enzyme-encoding locus using commonmutagenesis or knock-out technology. See, e.g., Methods in YeastGenetics (1997 edition), Adams, Gottschling, Kaiser, and Stems, ColdSpring Harbor Press (1998). In addition, certain point-mutation(s) canbe introduced which results in an enzyme with reduced activity.

Alternatively, antisense technology can be used to reduce enzymaticactivity. For example, yeast can be engineered to contain a cDNA thatencodes an antisense molecule that prevents an enzyme from being made.The term “antisense molecule” as used herein encompasses any nucleicacid molecule that contains sequences that correspond to the codingstrand of an endogenous polypeptide. An antisense molecule also can haveflanking sequences (e.g., regulatory sequences). Thus antisensemolecules can be ribozymes or antisense oligonucleotides. A ribozyme canhave any general structure including, without limitation, hairpin,hammerhead, or axhead structures, provided the molecule cleaves RNA.

Yeast having a reduced enzymatic activity can be identified using manymethods. For example, yeast having reduced pyruvate decarboxylaseactivity can be easily identified using common methods, which mayinclude, for example, measuring ethanol formation via gaschromatography.

Overexpression of Heterologous Genes

Methods for overexpressing a polypeptide from a native or heterologousnucleic acid molecule are well known. Such methods include, withoutlimitation, constructing a nucleic acid sequence such that a regulatoryelement promotes the expression of a nucleic acid sequence that encodesthe desired polypeptide. Typically, regulatory elements are DNAsequences that regulate the expression of other DNA sequences at thelevel of transcription. Thus, regulatory elements include, withoutlimitation, promoters, enhancers, and the like. For example, theexogenous genes can be under the control of an inducible promoter or aconstitutive promoter. Moreover, methods for expressing a polypeptidefrom an exogenous nucleic acid molecule in yeast are well known. Forexample, nucleic acid constructs that are used for the expression ofexogenous polypeptides within Kluyveromyces and Saccharomyces are wellknown (see, e.g., U.S. Pat. Nos. 4,859,596 and 4,943,529, forKluyveromyces and, e.g., Gellissen et al., Gene 190(1):87-97 (1997) forSaccharomyces). Yeast plasmids have a selectable marker and an origin ofreplication. In addition certain plasmids may also contain a centromericsequence. These centromeric plasmids are generally a single or low copyplasmid. Plasmids without a centromeric sequence and utilizing either a2 micron (S. cerevisiae) or 1.6 micron (K. lactis) replication originare high copy plasmids. The selectable marker can be eitherprototrophic, such as HIS3, TRP1, LEU2, URA3 or ADE2, or antibioticresistance, such as, bar, ble, hph, or kan.

In another embodiment, heterologous control elements can be used toactivate or repress expression of endogenous genes. Additionally, whenexpression is to be repressed or eliminated, the gene for the relevantenzyme, protein or RNA can be eliminated by known deletion techniques.

As described herein, any yeast within the scope of the disclosure can beidentified by selection techniques specific to the particular enzymebeing expressed, over-expressed or repressed. Methods of identifying thestrains with the desired phenotype are well known to those skilled inthe art. Such methods include, without limitation, PCR, RT-PCR, andnucleic acid hybridization techniques such as Northern and Southernanalysis, altered growth capabilities on a particular substrate or inthe presence of a particular substrate, a chemical compound, a selectionagent and the like. In some cases, immunohistochemistry and biochemicaltechniques can be used to determine if a cell contains a particularnucleic acid by detecting the expression of the encoded polypeptide. Forexample, an antibody having specificity for an encoded enzyme can beused to determine whether or not a particular yeast cell contains thatencoded enzyme. Further, biochemical techniques can be used to determineif a cell contains a particular nucleic acid molecule encoding anenzymatic polypeptide by detecting a product produced as a result of theexpression of the enzymatic polypeptide. For example, transforming acell with a vector encoding acetolactate synthase and detectingincreased acetolactate concentrations compared to a cell without thevector indicates that the vector is both present and that the geneproduct is active. Methods for detecting specific enzymatic activitiesor the presence of particular products are well known to those skilledin the art. For example, the presence of acetolactate can be determinedas described by Hugenholtz and Starrenburg, Appl. Microbiol. Biotechnol.38:17-22 (1992).

Increase of Enzymatic Activity

Yeast microorganisms of the invention may be further engineered to haveincreased activity of enzymes. The term “increased” as used herein withrespect to a particular enzymatic activity refers to a higher level ofenzymatic activity than that measured in a comparable yeast cell of thesame species. For example, overexpression of a specific enzyme can leadto an increased level of activity in the cells for that enzyme.Increased activities for enzymes involved in glycolysis or theisobutanol pathway would result in increased productivity and yield ofisobutanol.

Methods to increase enzymatic activity are known to those skilled in theart. Such techniques may include increasing the expression of the enzymeby increased copy number and/or use of a strong promoter, introductionof mutations to relieve negative regulation of the enzyme, introductionof specific mutations to increase specific activity and/or decrease theKm for the substrate, or by directed evolution. See, e.g., Methods inMolecular Biology (vol. 231), ed. Arnold and Georgiou, Humana Press(2003).

Carbon Source

The biocatalyst herein disclosed can convert various carbon sources intoisobutanol. The term “carbon source” generally refers to a substancesuitable to be used as a source of carbon for prokaryotic or eukaryoticcell growth. Carbon sources include, but are not limited to, biomasshydrolysates, starch, sucrose, cellulose, hemicellulose, xylose, andlignin, as well as monomeric components of these substrates. Carbonsources can comprise various organic compounds in various forms,including, but not limited to polymers, carbohydrates, acids, alcohols,aldehydes, ketones, amino acids, peptides, etc. These include, forexample, various monosaccharides such as glucose, dextrose (D-glucose),maltose, oligosaccharides, polysaccharides, saturated or unsaturatedfatty acids, succinate, lactate, acetate, ethanol, etc., or mixturesthereof. Photosynthetic organisms can additionally produce a carbonsource as a product of photosynthesis. In some embodiments, carbonsources may be selected from biomass hydrolysates and glucose.

The term “C2-compound” as used as a carbon source for engineered yeastmicroorganisms with mutations in all pyruvate decarboxylase (PDC) genesresulting in a reduction of pyruvate decarboxylase activity of saidgenes refers to organic compounds comprised of two carbon atoms,including but not limited to ethanol and acetate

The term “feedstock” is defined as a raw material or mixture of rawmaterials supplied to a microorganism or fermentation process from whichother products can be made. For example, a carbon source, such asbiomass or the carbon compounds derived from biomass are a feedstock fora microorganism that produces a biofuel in a fermentation process.However, a feedstock may contain nutrients other than a carbon source.

The term “traditional carbohydrates” refers to sugars and starchesgenerated from specialized plants, such as sugar cane, corn, and wheat.Frequently, these specialized plants concentrate sugars and starches inportions of the plant, such as grains, that are harvested and processedto extract the sugars and starches. Traditional carbohydrates are usedas food and also to a lesser extent as carbon sources for fermentationprocesses to generate biofuels, such as and chemicals

The term “biomass” as used herein refers primarily to the stems, leaves,and starch-containing portions of green plants, and is mainly comprisedof starch, lignin, cellulose, hemicellulose, and/or pectin. Biomass canbe decomposed by either chemical or enzymatic treatment to the monomericsugars and phenols of which it is composed (Wyman, C. E. 2003Biotechnological Progress 19:254-62). This resulting material, calledbiomass hydrolysate, is neutralized and treated to remove trace amountsof organic material that may adversely affect the biocatalyst, and isthen used as a feed stock for fermentations using a biocatalyst.

The term “starch” as used herein refers to a polymer of glucose readilyhydrolyzed by digestive enzymes. Starch is usually concentrated inspecialized portions of plants, such as potatoes, corn kernels, ricegrains, wheat grains, and sugar cane stems.

The term “lignin” as used herein refers to a polymer material, mainlycomposed of linked phenolic monomeric compounds, such as p-coumarylalcohol, coniferyl alcohol, and sinapyl alcohol, which forms the basisof structural rigidity in plants and is frequently referred to as thewoody portion of plants. Lignin is also considered to be thenon-carbohydrate portion of the cell wall of plants.

The term “cellulose” as used herein refers is a long-chain polymerpolysaccharide carbohydrate of beta-glucose of formula (C₆H₁₀O₅)n,usually found in plant cell walls in combination with lignin and anyhemicellulose.

The term “hemicellulose” refers to a class of plant cell-wallpolysaccharides that can be any of several heteropolymers. These includexylane, xyloglucan, arabinoxylan, arabinogalactan, glucuronoxylan,glucomannan and galactomannan. Monomeric components of hemicelluloseinclude, but are not limited to: D-galactose, L-galactose, D-mannose,L-rhamnose, L-fucose, D-xylose, L-arabinose, and D-glucuronic acid. Thisclass of polysaccharides is found in almost all cell walls along withcellulose. Hemicellulose is lower in weight than cellulose and cannot beextracted by hot water or chelating agents, but can be extracted byaqueous alkali. Polymeric chains of hemicellulose bind pectin andcellulose in a network of cross-linked fibers forming the cell walls ofmost plant cells.

Microorganism Characterized by Producing Isobutanol at High Yield

For a biocatalyst to produce isobutanol most economically, it is desiredto produce a high yield. Preferably, the only product produced isisobutanol. Extra products lead to a reduction in product yield and anincrease in capital and operating costs, particularly if the extraproducts have little or no value. Extra products also require additionalcapital and operating costs to separate these products from isobutanol.

The microorganism may convert one or more carbon sources derived frombiomass into isobutanol with a yield of greater than 5% of theoretical.In one embodiment, the yield is greater than 10%. In one embodiment, theyield is greater than 50% of theoretical. In one embodiment, the yieldis greater than 60% of theoretical. In another embodiment, the yield isgreater than 70% of theoretical. In yet another embodiment, the yield isgreater than 80% of theoretical. In yet another embodiment, the yield isgreater than 85% of theoretical. In yet another embodiment, the yield isgreater than 90% of theoretical. In yet another embodiment, the yield isgreater than 95% of theoretical. In still another embodiment, the yieldis greater than 97.5% of theoretical.

More specifically, the microorganism converts glucose, which can bederived from biomass into isobutanol with a yield of greater than 5% oftheoretical. In one embodiment, the yield is greater than 10% oftheoretical. In one embodiment, the yield is greater than 50% oftheoretical. In one embodiment the yield is greater than 60% oftheoretical. In another embodiment, the yield is greater than 70% oftheoretical. In yet another embodiment, the yield is greater than 80% oftheoretical. In yet another embodiment, the yield is greater than 85% oftheoretical. In yet another embodiment the yield is greater than 90% oftheoretical. In yet another embodiment, the yield is greater than 95% oftheoretical. In still another embodiment, the yield is greater than97.5% of theoretical

Microorganism Expressing a Cytosolically Localized Acetolactate Synthase(ALS)

In yeasts such as S. cerevisiae, the native acetolactate synthase,encoded in S. cerevisiae by the ILV2 gene, is naturally expressed in theyeast mitochondria. Unlike the endogenous acetolactate synthase ofyeast, expression of heterologous, acetolactate synthases such as the B.subtilis alsS and the L. lactis alsS in yeast occurs in the yeastcytosol (i.e. cytosolically-localized). Thus, cytosolic expression ofacetolactate synthase is achieved by transforming a yeast with a geneencoding an acetolactate synthase protein (EC 2.2.1.6).

ALS homologs that could be cytosolically expressed and localized inyeast are predicted to lack a mitochondrial targeting sequence asanalyzed using mitoprot (Claros et al., 1996, Eur. J. Biochem 241:779-86). Such cytosolically localized ALS proteins can be used as thefirst step in the isobutanol pathway. ALS homologs include, but are notlimited to, the following: the Serratia marcescens ALS (GenBankAccession No. ADH43113.1) (probability of mitochondrial localization0.07), the Enterococcus faecalis ALS (GenBank Accession No.NP_(—)814940) (probability of mitochondrial localization 0.21), theLeuconostoc mesenteroides (GenBank Accession No. YP_(—)818010.1)(probability of mitochondrial localization 0.21), the Staphylococcusaureus ALS (GenBank Accession No. YP_(—)417545) (probability ofmitochondrial localization 0.13), the Burkholderia cenocepacia ALS(GenBank Accession No. YP_(—)624435) (probability of mitochondriallocalization 0.15), Trichoderma atroviride ALS (SEQ ID NO: 77)probability of mitochondrial localization 0.19), Talaromyces stipitatusALS (SEQ ID NO: 78) (probability of mitochondrial localization 0.19),and Magnaporthe grisea ALS (GenBank Accession No. EDJ99221) (probabilityof mitochondrial localization 0.02).

In alternative embodiments described herein, an ALS enzyme that ispredicted to be mitochondrially localized may be mutated or modified toremove or modify an N-terminal mitochondrial targeting sequence (MTS) toremove or eliminate its ability to target the ALS enzyme to themitochondria. Removal of the MTS can increase cytosolic localization ofthe ALS and/or increase the cytosolic activity of the ALS as compared tothe parental ALS.

Methods for gene expression in yeasts are known in the art (See, e.g.,Methods in Enzymology, 2004, Vol 194, Guide to Yeast Genetics andMolecular and Cell Biology). As is understood in the art, the expressionof heterologous, prokaryotic genes in yeast typically requires apromoter, operably linked to a coding region of interest, and atranscriptional terminator. A number of yeast promoters can be used inconstructing expression cassettes for genes encoding an acetolactatesynthase, including, but not limited to constitutive promoters FBA,GPD1, ADH1, and GPM, and the inducible promoters GAL1, GAL10, and CUP1.Suitable transcriptional terminators include, but are not limited toFBA, GPD, GPM, ERG10, GAL1, CYC1, and ADH1.

Microorganism Characterized by Production of Isobutanol from Pyruvatevia an Overexpressed Isobutanol Pathway and a Pdc-Minus Phenotype

In yeast, the conversion of pyruvate to acetaldehyde is a major drain onthe pyruvate pool (FIG. 2), and, hence, a major source of competitionwith the isobutanol pathway. This reaction is catalyzed by the pyruvatedecarboxylase (PDC) enzyme. Reduction of this enzymatic activity in theyeast microorganism results in an increased availability of pyruvate andreducing equivalents to the isobutanol pathway and may improveisobutanol production and yield in a yeast microorganism that expressesa pyruvate-dependent isobutanol pathway (FIG. 3).

Reduction of PDC activity can be accomplished by 1) mutation or deletionof a positive transcriptional regulator for the structural genesencoding for PDC or 2) mutation or deletion of all PDC genes in a givenorganism. The term “transcriptional regulator” can specify a protein ornucleic acid that works in trans to increase or to decrease thetranscription of a different locus in the genome. For example, in S.cerevisiae, the PDC2 gene, which encodes for a positive transcriptionalregulator of PDC1,5,6 genes can be deleted; a S. cerevisiae in which thePDC2 gene is deleted is reported to have only ˜10% of wildtype PDCactivity (Hohmann, Mol Gen Genet, 241:657-666 (1993)). Alternatively,for example, all structural genes for PDC (e.g. in S. cerevisiae, PDC1,PDC5, and PDC6, or in K. lactis, PDC1) are deleted.

Crabtree-positive yeast strains such as S. cerevisiae strain thatcontains disruptions in all three of the PDC alleles no longer produceethanol by fermentation. However, a downstream product of the reactioncatalyzed by PDC, acetyl-CoA, is needed for anabolic production ofnecessary molecules. Therefore, the Pdc-mutant is unable to grow solelyon glucose, and requires a two-carbon carbon source, either ethanol oracetate, to synthesize acetyl-CoA. (Flikweert M T, de Swaaf M, vanDijken J P, Pronk J T. FEMS Microbiol Lett. 1999 May 1; 174(1):73-9.PMID:10234824 and van Maris A J, Geertman J M, Vermeulen A, GroothuizenM K, Winkler A A, Piper M D, van Dijken J P, Pronk J T. Appl EnvironMicrobiol. 2004 January; 70(1):159-66. PMID: 14711638).

Thus, in an embodiment, such a Crabtree-positive yeast strain may beevolved to generate variants of the PDC mutant yeast that do not havethe requirement for a two-carbon molecule and has a growth rate similarto wild type on glucose. Any method, including chemostat evolution orserial dilution may be utilized to generate variants of strains withdeletion of three PDC alleles that can grow on glucose as the solecarbon source at a rate similar to wild type (van Maris et al., DirectedEvolution of Pyruvate Decarboxylase-Negative Saccharomyces cerevisiae,Yielding a C2-Independent, Glucose-Tolerant, and Pyruvate-HyperproducingYeast, Applied and Environmental Microbiology, 2004, 70(1), 159-166).

Microorganism Characterized by Production of Isobutanol from Pyruvatevia an Overexpressed Isobutanol Pathway and a PDC-Minus GPD-MinusPhenotype

Another pathway for NADH oxidation is through the production ofglycerol. Dihydroxyacetone-phosphate, an intermediate of glycolysis isreduced to glycerol 3-phosphate by glycerol 3-phosphate dehydrogenase(GPD). Glycerol 3-phosphatase (GPP) converts glycerol 3-phosphate toglycerol. This pathway consumes carbon from glucose as well as reducingequivalents (NADH) resulting in less pyruvate and reducing equivalentsavailable for the isobutanol pathway. These pathways contribute to lowyield and low productivity of isobutanol. Accordingly, deletions of PDCand GPD would increase yield and productivity of isobutanol. Asexemplified in Examples 9 and 13, the yield may increase to 70% by theadditional deletion of GPD. In an embodiment, a yeast microorganism mayinclude a recombinant microorganism having an engineered pathway toconvert a carbon source, such as glucose, to isobutanol.

Looking at FIG. 4, an additional deletion of GPD results in a reductionin the production of glycerol 3-phosphate and glycerol. This results inan increase in the amount of carbon from glucose being converted topyruvate and also a decrease in the consumption of reducing equivalents.Both of these factors combined results in a further increase in yield ofisobutanol.

Yield of isobutanol can be increased also by reduction of the glycerol3-phosphate dehydrogenase (GPD, EC1.1.1.8) activity, which is involvedin the production of glycerol (FIG. 2). This enzyme catalyzes thereduction of the glycolysis intermediate, dihydroxyacetone-phosphate, toglycerol 3-phosphate. In this reaction, an NADH is oxidized to NAD+.Therefore, glycerol production would be a drain on the reducingequivalent (NADH) as well as on the carbon from glucose. This pathwaycan be eliminated by deleting the glycerol-3-phosphate dehydrogenases(e.g. GPD1 and GPD2 in S. cerevisiae, GPD1 in K. lactis) in the yeast.

Additionally, activities of other gene products may function as drainson metabolic intermediates. For example, reductions of the followingactivities may increase yield of isobutanol. Pyruvate dehydrogenase(PDH) activity, supplied by a multi-gene product complex, representsanother route of pyruvate dissimilation. Reduction of PDH activity mayincrease pyruvate availability. Branched-chain amino acid transaminase(EC 2.6.1.42) interconverts valine⇄keto-isovalerate in the cytosol, andmay therefore reduce or limit available keto-isovalerate to isobutanolpathway. 3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11)directs the isobutanol pathway intermediate, keto-isovalerate, to thecoenzyme A synthesis pathway. Alphaisopropylmalate isomerase (EC4.1.3.12) directs the isobutanol pathway intermediate, keto-isovalerate,to the synthesis of leucine. Therefore, all of these enzymaticactivities represent possible additional targets for disruption,deletion, or both.

Microorganism Characterized by Production of Isobutanol from Pyruvatevia an Overexpressed Balanced Isobutanol Pathway and a PDC-MinusGPD-Minus Phenotype

To further increase yield from the pathway the imbalance in the use ofreducing equivalents need to be corrected. Glycolysis generates 2 molesNADHs and 2 moles of pyruvate per mole of glucose, while the isobutanolpathway consumes either 2 NADPHs or 1 NADH and 1 NADPH for every 2 molesof pyruvate utilized. KARI enzymes typically use NADPH. There existsboth an NADH and NADPH dependent alcohol dehydrogenase that can be usedfor the isobutanol pathway. For example, S. cerevisiae Adh2p is anNADH-dependent enzyme that is able to reduce isobutyraldehyde toisobutanol. Alternatively, this conversion can be performed by S.cerevisiae Adh6p or Adh7p, which are NADPH-dependent alcoholdehydrogenases. The additional NADPH can be obtained from the pentosephosphate pathway, but this results in a reduced yield as only 5 molesof pyruvate is generated from 3 moles of glucose, while glycolysisgenerates 6 moles of pyruvate from 3 moles of glucose.

This imbalance can be balanced in several ways. In one embodiment,glycolysis can be engineered to generate NADPH instead of NADH. This isaccomplished by replacing the endogenous NAD+-dependent glyceraldehydes3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12) with an NADP+-dependentGAPDH (EC 1.2.1.13). Such NADP+-dependent GAPDHs have been identified inbacteria (i.e. gapB in B. subtilis), yeast (GDP1 in K. lactis) andplants. (Fillinger et al., J Biol Chem. 275:14031-14037, Verho et al.,Biochemistry, 41:13833-13838) This may result in glycolysis producing 2moles of NADPH which balances the 2 moles of NADPH that are consumed bythe isobutanol pathway utilizing an NADPH-dependent alcoholdehydrogenase. See, for example, Richard, et al, U.S. Patent ApplicationPublication Number US 2005/0106734 A1. In addition to balancing thepathway, this method may result in the reduction of available NADH andhence a reduction in the ability of the glycerol 3-phosphatedehydrogenase to generate glycerol.

In a second embodiment, an NADP⁺-dependent GAPDH is co-expressed withthe endogenous NAD⁺-dependent GAPDH. This may allow the production ofboth NADPH and NADH from glycolysis and balance the consumption of 1mole of NADPH and 1 mole of NADH by an isobutanol pathway utilizing anNADH-dependent alcohol dehydrogenase.

In yet another embodiment, the NADPH-dependent KARI enzyme in thepathway is engineered to use NADH. This has been shown with the E. coliKARI (ilvC) (Rane M J and Calvo K C, Arch Biochem Biophys.,338(1):83-89). Alternatively, a KARI from Methanococcus species can beused. These KARI enzymes have been reported to be able to utilize NADHwith roughly 60% the activity with NADPH (Xing et al., Journal ofBacteriology 1990). The use of these NADH-utilizing i/vC in combinationwith an NADH-dependent alcohol dehydrogenase also balances theNADH/NADPH imbalance.

Furthermore any of the genes encoding the foregoing enzymes (or anyothers mentioned herein (or any of the regulatory elements that controlor modulate expression thereof) may be subject to directed evolutionusing methods known to those of skill in the art. Such action allowsthose of skill in the art to optimize the enzymes for expression andactivity in yeast.

In addition, genes encoding these enzymes can be identified from otherfungal and bacterial species and can be expressed for the modulation ofthis pathway. A variety of organisms could serve as sources for theseenzymes, including, but not limited to, Saccharomyces spp., including S.cerevisiae and S. uvarum, Kluyveromyces spp., including K.thermotolerans, K. lactis, and K. marxianus, Pichia spp., Hansenulaspp., including H. polymorpha, Candida spp., Trichosporon spp.,Yamadazyma spp., including Y. stipitis, Torulaspora pretoriensis,Schizosaccharomyces spp., incl. Schizosaccharomyces pombe, Cryptococcusspp., Aspergillus spp., Neurospora spp. or Ustilago spp. Sources ofgenes from anaerobic fungi include, but not limited to, Piromyces spp.,Orpinomyces spp., or Neocallimastix spp. Sources of prokaryotic enzymesthat are useful include, but not limited to, Escherichia coli, Zymomonasmobilis, Staphylococcus aureus, Bacillus spp., Clostridium spp.,Corynebacterium spp., Pseudomonas spp., Lactococcus spp., Enterobacterspp., and Salmonella spp.

Microorganism Characterized by Balanced Isobutanol Pathway

In the various embodiments described herein, the engineered metabolicpathway may be balanced with respect to NADH and NADPH as compared to anative or unmodified metabolic isobutanol pathway from a correspondingparental microorganism, wherein the native or unmodified metabolicpathway is not balanced with respect to NADH and NADPH.

The ideal production microorganism produces a desirable product at closeto theoretical yield. For example the ideal isobutanol producingorganism produces isobutanol according to the following equation: 1glucose→isobutanol+2 CO₂+H₂O.

Accordingly, 66% of the glucose carbon results in isobutanol, while 33%is lost as CO₂. In exemplary metabolic pathways for the conversion ofpyruvate to isobutanol described by Atsumi et al. (WO/2008/098227, andAtsumi et al., Nature, 2008 Jan. 3; 451(7174):86-9), two of the fiveenzymes used to convert pyruvate into isobutanol according to themetabolic pathway outlined in FIG. 1 require the reduced cofactornicotinamide adenine dinucleotide phosphate (NADPH). NADPH is producedonly sparingly by the cell—the reduced cofactor nicotinamide adeninedinucleotide (NADH) is the preferred equivalent. Respiration is requiredto produce NADPH in the large quantities required to support high-levelproduction of isobutanol.

Even if competing pathways can be eliminated or reduced in activity bymetabolic engineering, yield is limited to about 83% of theoretical.Carbon loss to carbon dioxide (CO₂) remains the main limitation on yieldin the aforementioned metabolic pathway for the production ofisobutanol. Reducing the oxygen uptake rate (OUR) of the cells shoulddecrease the loss of carbon to CO₂ because it decreases the metabolicflux through the CO₂-generating tricarboxylic acid (TCA) cycle and/orpentose phosphate pathway (PPP). However, a modified microorganismutilizing the aforementioned metabolic pathway for the production ofisobutanol exhibits drastically decreased specific productivity underconditions where the OUR is decreased and isobutanol production underanaerobic conditions may not be possible.

The decreased yield and the loss of productivity upon O₂ limitationindicate that the strain uses one or more metabolic pathways to generatethe NADPH needed to support isobutanol production. In a modified cellutilizing the aforementioned metabolic pathway the production ofisobutanol from glucose results in an imbalance between the cofactorsreduced during glycolysis and the cofactors oxidized during theconversion of pyruvate to isobutanol. While glycolysis produces twomoles of NADH, the isobutanol pathway consumes two moles of NADPH. Thisleads to a deficit of two moles of NADPH and overproduction of two molesof NADH per isobutanol molecule produced, a state described henceforthas cofactor imbalance.

The terms “cofactor balance” or “balanced with respect to cofactorusage” refer to a recombinant microorganism comprising a metabolicpathway converting a carbon source to a fermentation product and amodification that leads to the regeneration of all redox cofactorswithin the recombinant microorganism producing said fermentation productfrom a carbon source and wherein the re-oxidation or re-reduction ofsaid redox cofactors does not require the pentose phosphate pathway, theTCA cycle or the generation of additional fermentation products.

Stated another way, the terms “cofactor balance” or “balanced withrespect to cofactor usage” can refer to an advantageous modificationthat leads to the regeneration of all redox cofactors within therecombinant microorganism producing a fermentation product from a carbonsource and wherein said re-oxidation or re-reduction of all redoxcofactors does not require the production of byproducts or co-products.

Stated another way, the terms “cofactor balance” or “balanced withrespect to cofactor usage” can refer to an advantageous modificationthat leads to the regeneration of all redox cofactors within therecombinant microorganism producing a fermentation product from a carbonsource under anaerobic conditions and wherein the production ofadditional fermentation products is not required for re-oxidation orre-reduction of redox cofactors.

Stated another way, the terms “cofactor balance” or “balanced withrespect to cofactor usage” can refer to an advantageous modificationthat leads to the regeneration of all redox cofactors within therecombinant microorganism producing a fermentation product from a carbonsource and wherein said modification increases production of saidfermentation product under anaerobic conditions compared to the parentalor wild type microorganism and wherein additional fermentation productsare not required for the regeneration of said redox cofactors.

The cell has several options for resolving a cofactor imbalance. One isto change the relative fluxes going from glucose through glycolysis andthrough the pentose phosphate pathway (PPP). For each glucose moleculemetabolized through the PPP, two moles of NADPH are generated inaddition to the two moles of NADH that are generated through glycolysis(a total of 4 reducing equivalents). Therefore, use of the PPP resultsin the generation of excess reducing equivalents since only two molesare consumed during the production of isobutanol. Under anaerobicconditions, and without an alternate electron acceptor, the cell has noway to reoxidize or regenerate these extra cofactors to NADP⁺ andmetabolism thus stops. The excess reducing equivalents must instead beutilized for energy production through aerobic respiration which is onlypossible under aerobic conditions or for the production of byproducts.Another result of the flux through the PPP is that one additionalmolecule of CO₂ is lost per molecule of glucose consumed, which limitsthe yield of isobutanol that can be achieved under aerobic conditions.

Another way the cell can generate NADPH is via the TCA cycle. Fluxthrough the TCA cycle results in carbon loss through CO₂ and inproduction of NADH in addition to the NADPH required for the isobutanolpathway. The NADH would have to be utilized for energy productionthrough respiration under aerobic conditions (and without an alternateelectron acceptor) or for the production of byproducts. In addition, theTCA cycle likely is not functional under anaerobic conditions and istherefore unsuitable for the production of stoichiometric amounts ofNADPH in an anaerobic isobutanol process.

An economically competitive isobutanol process requires a high yieldfrom a carbon source. Lower yield means that more feedstock is requiredto produce the same amount of isobutanol. Feedstock cost is the majorcomponent of the overall operating cost, regardless of the nature of thefeedstock and its current market price. From an economical perspective,this is important because the cost of isobutanol is dependent on thecost of the biomass-derived sugars. An increase in feedstock costresults in an increase in isobutanol cost. Thus, it is desirable toutilize NADH-dependent enzymes for the conversion of pyruvate toisobutanol.

An enzyme is “NADH-dependent” if it catalyzes the reduction of asubstrate coupled to the oxidation of NADH with a catalytic efficiencythat is greater than the reduction of the same substrate coupled to theoxidation of NADPH at equal substrate and cofactor concentrations.

Thus, in one embodiment of the invention, a microorganism is provided inwhich cofactor usage is balanced during the production of a fermentationproduct.

In a specific aspect, a microorganism is provided in which cofactorusage is balanced during the production of isobutanol, in this case,production of isobutanol from pyruvate utilizes the same cofactor thatis produced during glycolysis.

In another embodiment, a microorganism is provided in which cofactorusage is balanced during the production of a fermentation product andthe microorganism produces the fermentation product at a higher yieldcompared to a modified microorganism in which the cofactor usage in notbalanced.

In a specific aspect, a microorganism is provided in which cofactorusage is balanced during the production of isobutanol and themicroorganism produces isobutanol at a higher yield compared to amodified microorganism in which the cofactor usage in not balanced.

In yet another embodiment, a modified microorganism in which cofactorusage is balanced during the production of a fermentation product mayallow the microorganism to produce said fermentation product underanaerobic conditions at higher rates, and yields as compared to amodified microorganism in which the cofactor usage in not balancedduring production of a fermentation product.

In a specific aspect, a modified microorganism in which cofactor usageis balanced during the production of isobutanol may allow themicroorganism to produce isobutanol under anaerobic conditions at higherrates, and yields as compared to a modified microorganism in which thecofactor usage is not balanced during production of isobutanol.

One compound to be produced by the recombinant microorganism accordingto the present invention is isobutanol. However, the present inventionis not limited to isobutanol. The invention may be applicable to anymetabolic pathway that is imbalanced with respect to cofactor usage. Oneskilled in the art is able to identify pathways that are imbalanced withrespect to cofactor usage and apply this invention to providerecombinant microorganisms in which the same pathway is balanced withrespect to cofactor usage. One skilled in the art will recognize thatthe identified pathways may be of longer or shorter length, contain moreor fewer genes or proteins, and require more or fewer cofactors than theexemplary isobutanol pathway. Further, one skilled in the art willrecognize that in certain embodiments, such as a recombinant microbialhost that produces an excess of NADPH, certain embodiments of thepresent invention may be adapted to convert NADPH to NADH.

Microorganisms Characterized by Providing Cofactor Balance viaEngineered Enzymes

Conversion of one mole of glucose to two moles of pyruvate viaglycolysis leads to the production of two moles of NADH. A metabolicpathway that converts pyruvate to a target product that consumes eithertwo moles of NADPH or one mole of NADH and one mole of NADPH leads tocofactor imbalance. One example of such a metabolic pathway is theisobutanol metabolic pathway described by Atsumi et al. (Atsumi et al.,2008, Nature 451: 86-9), which converts two moles of pyruvate to onemole of isobutanol. In this five enzyme pathway, two enzymes aredependent upon NADPH: (1) KARI and (2) ADH, encoded by the E. coli ilvCand E. coli yqhD, respectively.

To resolve this cofactor imbalance, the present invention provides arecombinant microorganism in which the NADPH-dependent enzymes KARI andADH are replaced with enzymes that preferentially depend on NADH (i.e.KARI and ADH enzymes that are NADH-dependent).

To further resolve this cofactor imbalance, the present invention inanother embodiment provides recombinant microorganisms wherein theNADH-dependent KARI and ADH enzymes are overexpressed.

In one aspect, such enzymes may be identified in nature. In analternative aspect, such enzymes may be generated by protein engineeringtechniques including but not limited to directed evolution orsite-directed mutagenesis.

In one embodiment, the two NADPH-dependent enzymes within an isobutanolbiosynthetic pathway that converts pyruvate to isobutanol may bereplaced with ones that utilize NADH. These two enzymes may be KARI andan alcohol dehydrogenase (ADH).

In another embodiment, two NADH-dependent enzymes that catalyze the samereaction as the NADH-dependent enzymes are overexpressed. These twoenzymes may be KARI and an alcohol dehydrogenase.

In one aspect, NADH-dependent KARI and ADH enzymes are identified innature. In another aspect, the NADPH-dependent KARI and ADH enzymes maybe engineered using protein engineering techniques including but notlimited to directed evolution and site-directed mutagenesis.

There exist two basic options for engineering NADH-dependentisobutyraldehyde dehydrogenases or ketol-acid reductoisomerases: (1)increase the NADH-dependent activity of an NADPH-dependent enzyme thatis active towards the substrate of interest and/or (2) increase theactivity of an NADH-dependent enzyme that is not sufficiently activetowards the substrate of interest.

There exist two basic options for engineering NADH-dependentisobutyraldehyde dehydrogenases or ketol-acid reductoisomerases: (1)increase the NADH-dependent activity of an NADPH-dependent enzyme thatis active towards the substrate of interest and/or (2) increase theactivity of an NADH-dependent enzyme that is not sufficiently activetowards the substrate of interest.

NADH-Dependent KARI Enzymes

As shown in FIG. 1, the ketol-acid reductoisomerase (KARI) enzyme of theisobutanol biosynthetic pathway as disclosed by Atsumi et al. (Atsumi etal., 2008, Nature 45: 86-9), requires the cofactor nicotinamidedinucleotide phosphate (NADPH) to convert acetolactate to 2,3-dihydroxyisovalerate. However, under anaerobic conditions, NADPH isproduced only sparingly by the cell—nicotinamide adenine dinucleotide(NADH) is the preferred equivalent. Therefore, oxygen is required toproduce NADPH in the large quantities to support high-level productionof isobutanol. Thus, the production of isobutanol is feasible only underaerobic conditions and the maximum yield that can be achieved with thispathway is limited. Accordingly, KARI enzymes that preferentiallyutilize NADH rather than NADPH are desirable.

Other biosynthetic pathways utilize KARI enzymes for the conversion ofacetolactate to 2, 3-dihydroxyisovalerate. For example, KARI enzymesconvert acetolactate to 2, 3-dihydroxyisovalerate as part of thebiosynthetic pathway for the production of 3-methyl-1-butanol (Atsumi etal., 2008, Nature 45: 86-9).

Yet other biosynthetic pathways utilize KARI to convert2-aceto-2-hydroxy-butyrate to 2, 3-dihydroxy-3-methylvalerate. Thisreaction is part of the biosynthetic pathway for the production of2-methyl-1-butanol. (Atsumi et al., 2008, Nature 45: 86-9).

As used herein, the term “KARI” or “KARI enzyme” or “ketol-acidreductoisomerase” are used interchangeably herein to refer to an enzymethat catalyzes the conversion of acetolactate to 2,3-dihydroxyisovalerate and/or the conversion of2-aceto-2-hydroxy-butyrate to 2, 3-dihydroxy-3-methylvalerate. Moreover,these terms can be used interchangeably herein with the terms“acetohydroxy acid isomeroreductase” and “acetohydroxy acidreductoisomerase.”

Enzymes for use in the compositions and methods of the invention includeany enzyme having the ability to convert acetolactate to2,3-dihydroxyisovalerate and/or the ability to convert2-aceto-2-hydroxy-butyrate to 2,3-dihydroxy-3-methylvalerate. Suchenzymes include, but are not limited to, the E. coli ilvC gene productand the S. cerevisiae ILV5 gene product, and the KARI enzyme fromPiromyces sp, Buchnera aphidicola, Spinacia oleracea, Oryza sativa,Chlamydomonas reinhardtii, Neurospora crassa, Schizosaccharomyces pombe,Laccaria bicolor, Ignicoccus hospitalis, Picrophilus torridus,Acidiphilium cryptum, Cyanobacteria/Synechococcus sp., Zymomonasmobilis, Bacteroides thetaiotaomicron, Methanococcus maripaludis, Vibriofischeri, Shewanella sp, Gramella forsetti, Psychromonas ingrhamaii, andCytophaga hutchinsonii.

KARI sequences are available from a vast array of microorganisms,including, but not limited to, Escherichia coli (GenBank Nos:NP_(—)418222 and NC_(—)000913, Saccharomyces cerevisiae (GenBank Nos:NP_(—)013459 and NC_(—)001144, Methanococcus maripaludis (GenBank Nos:CAF30210 and BX957220, and Bacillus subtilis (GenBank Nos: CAB14789 andZ99118) and the KARI enzymes from Piromyces sp (GenBank No: CAA76356),Buchnera aphidicola (GenBank No: AAF13807), Spinacia oleracea (GenBankNos: Q01292 and CAA40356), Oryza sativa (GenBank No: NP_(—)001056384)Chlamydomonas reinhardtii (GenBank No: XP_(—)001702649), Neurosporacrassa (GenBank No: XP_(—)961335), Schizosaccharomyces pombe (GenBankNo: NP_(—)001018845), Laccaria bicolor (GenBank No: XP_(—)001880867),Ignicoccus hospitalis (GenBank No: YP_(—)001435197), Picrophilustorridus (GenBank No: YP_(—)023851), Acidiphilium cryptum (GenBank No:YP_(—)001235669), Cyanobacteria/Synechococcus sp. (GenBank No:YP_(—)473733), Zymomonas mobilis (GenBank No: YP_(—)162876), Bacteroidesthetaiotaomicron (GenBank No: NP_(—)810987), Methanococcus maripaludis(GenBank No: YP_(—)001097443), Vibrio fischeri (GenBank No:YP_(—)205911), Shewanella sp (GenBank No: YP_(—)732498), Gramellaforsetti (GenBank No: YP_(—)862142), Psychromonas ingrhamaii (GenBankNo: YP_(—)942294), and Cytophaga hutchinsonii (GenBank No:YP_(—)677763).

As will be understood by one of ordinary skill in the art, modified KARIenzymes may be obtained by recombinant or genetic engineering techniquesthat are routine and well-known in the art. Mutant KARI enzymes can, forexample, be obtained by mutating the gene or genes encoding the KARIenzyme of interest by site-directed or random mutagenesis. Suchmutations may include point mutations, deletion mutations andinsertional mutations. For example, one or more point mutations (e.g.,substitution of one or more amino acids with one or more different aminoacids) may be used to construct mutant KARI enzymes of the invention.

Ketol-acid reductoisomerase (KARI) catalyzes the reduction ofacetolactate to 2, 3-dihydroxyisovalerate. The two-step reactioninvolves an alkyl migration and a ketone reduction that occurs at asingle active site on the enzyme without dissociation of any reactionintermediates. The enzyme is NADPH-dependent. The cofactor specificitymay be expanded or switched so that it will utilize both cofactors andpreferentially NADH during the production of isobutanol. A studypublished in 1997 (Rane, M. J. and K. C. Calvo, Archives of Biochemistryand Biophysics, 1997. 338: p. 83-89) describes a supposedcofactor-switched KARI quadruplet variant of the E. coli ilvC geneproduct with mutations R68D, K69L, K75V and R76D). However, in-housestudies indicate that although the ratio NADH/NADPH was 2.5, thespecific activity of this variant on NADH was actually worse thanwildtype, rendering this enzyme not suited for the purpose of thisdisclosure.

Modified or Mutated KARI Enzymes

In accordance with the invention, any number of mutations can be made tothe KARI enzymes, and in a preferred aspect, multiple mutations can bemade to result in an increased ability to utilize NADH for theconversion of acetolactate to 2,3-dihydroxyisovalerate. Such mutationsinclude point mutations, frame shift mutations, deletions, andinsertions, with one or more (e.g., one, two, three, or four, etc.)point mutations preferred.

Mutations may be introduced into the KARI enzymes of the presentinvention using any methodology known to those skilled in the art.Mutations may be introduced randomly by, for example, conducting a PCRreaction in the presence of manganese as a divalent metal ion cofactor.Alternatively, oligonucleotide directed mutagenesis may be used tocreate the mutant KARI enzymes which allows for all possible classes ofbase pair changes at any determined site along the encoding DNAmolecule. In general, this technique involves annealing anoligonucleotide complementary (except for one or more mismatches) to asingle stranded nucleotide sequence coding for the KARI enzyme ofinterest. The mismatched oligonucleotide is then extended by DNApolymerase, generating a double-stranded DNA molecule which contains thedesired change in sequence in one strand. The changes in sequence can,for example, result in the deletion, substitution, or insertion of anamino acid. The double-stranded polynucleotide can then be inserted intoan appropriate expression vector, and a mutant or modified polypeptidecan thus be produced. The above-described oligonucleotide directedmutagenesis can, for example, be carried out via PCR.

The invention further includes homologous KARI enzymes which are 5%,10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%,98%, or 99% identical at the amino acid level to a wild-type KARI enzyme(e.g., encoded by the Ec_ilvC gene or S. cerevisiae ilv5 gene) andexhibit an increased ability to utilize NADH for the conversion ofacetolactate to 2,3-dihydroxyisovalerate. Also included within theinvention are KARI enzymes which are 50%, 60%, 70%, 75%, 80%, 85%, 90%,95%, 96%, 97%, 98%, or 99% identical at the amino acid level to a KARIenzyme comprising the amino acid sequence set out in SEQ ID NO: 56 andexhibit an increased ability to utilize NADH for the conversion ofacetolactate to 2,3-dihydroxyisovalerate. The invention also includesnucleic acid molecules which encode the above described KARI enzymes.

The invention also includes fragments of KARI enzymes which comprise atleast 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, or 600 aminoacid residues and retain one or more activities associated with KARIenzymes. Such fragments may be obtained by deletion mutation, byrecombinant techniques that are routine and well-known in the art, or byenzymatic digestion of the KARI enzyme(s) of interest using any of anumber of well-known proteolytic enzymes. The invention further includesnucleic acid molecules which encode the above described mutant KARIenzymes and KARI enzyme fragments.

By a protein or protein fragment having an amino acid sequence at least,for example, 50% “identical” to a reference amino acid sequence it isintended that the amino acid sequence of the protein is identical to thereference sequence except that the protein sequence may include up to 50amino acid alterations per each 100 amino acids of the amino acidsequence of the reference protein. In other words, to obtain a proteinhaving an amino acid sequence at least 50% identical to a referenceamino acid sequence, up to 50% of the amino acid residues in thereference sequence may be deleted or substituted with another aminoacid, or a number of amino acids up to 50% of the total amino acidresidues in the reference sequence may be inserted into the referencesequence. These alterations of the reference sequence may occur at theamino (N—) and/or carboxy (C—) terminal positions of the reference aminoacid sequence and/or anywhere between those terminal positions,interspersed either individually among residues in the referencesequence and/or in one or more contiguous groups within the referencesequence. As a practical matter, whether a given amino acid sequence is,for example, at least 50% identical to the amino acid sequence of areference protein can be determined conventionally using known computerprograms such as those described above for nucleic acid sequenceidentity determinations, or using the CLUSTAL W program (Thompson, J.D., et al., Nucleic Acids Res. 22:4673 4680 (1994)).

In one aspect, amino acid substitutions are made at one or more of theabove identified positions (i.e., amino acid positions equivalent orcorresponding to A71, R76, S78, or Q110 of E. coli IlvC). Thus, theamino acids at these positions may be substituted with any other aminoacid including Ala, Asn, Arg, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu,Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, and Val. A specific example of aKARI enzyme which exhibits an increased ability to utilize NADH includesan E. coli IlvC KARI enzyme in which (1) the alanine at position 71 hasbeen replaced with a serine, (2) the arginine at position 76 has beenreplaced with an aspartic acid, (3) the serine at position 78 has beenreplaced with an aspartic acid, and/or (4) the glutamine at position 110has been replaced with valine (as described in commonly owned andco-pending applications U.S. Ser. No. 12/610,784 and PCT/US09/62952(published as WO/2010/051527).

Polypeptides having the ability to convert acetolactate to2,3-dihydroxyisovalerate and/or 2-aceto-2-hydroxy-butyrate to2,3-dihydroxy-3-methylvalerate for use in the invention may be isolatedfrom their natural prokaryotic or eukaryotic sources according tostandard procedures for isolating and purifying natural proteins thatare well-known to one of ordinary skill in the art (see, e.g., Houts, G.E., et al., J. Virol. 29:517 (1979)). In addition, polypeptides havingthe ability to convert acetolactate to 2,3-dihydroxyisovalerate and/or2-aceto-2-hydroxy-butyrate to 2,3-dihydroxy-3-methylvalerate may beprepared by recombinant DNA techniques that are familiar to one ofordinary skill in the art (see, e.g., Kotewicz, M. L., et al., Nucl.Acids Res. 16:265 (1988); Soltis, D. A., and Skalka, A. M., Proc. Natl.Acad. Sci. USA 85:3372 3376 (1988)).

In accordance with the invention, one or more mutations may be made inany KARI enzyme of interest in order to increase the ability of theenzyme to utilize NADH, or confer other properties described herein uponthe enzyme, in accordance with the invention. Such mutations includepoint mutations, frame shift mutations, deletions and insertions.Preferably, one or more point mutations, resulting in one or more aminoacid substitutions, are used to produce KARI enzymes having an enhancedor increased ability to utilize NADH, particularly to facilitate theconversion of acetolactate to 2,3-dihydroxyisovalerate and/or theconversion of 2-aceto-2-hydroxy-butyrate to2,3-dihydroxy-3-methylvalerate. In a preferred aspect of the invention,one or more mutations at positions equivalent or corresponding toposition A71 (e.g., A71S), R76 (e.g., R76D), S78 (e.g. S78D), and/orQ110 (e.g. Q110V) and/or D146 (e.g. D146G), and/or G185 (e.g. G185R)and/or K433 (e.g. K433E) of the E. coli IlvC KARI enzyme may be made toproduce the desired result in other KARI enzymes of interest.

The corresponding positions of the KARI enzymes identified herein (e.g.E. coli IlvC may be readily identified for other KARI enzymes by one ofskill in the art. Thus, given the defined region and the assaysdescribed in the present application, one with skill in the art can makeone or a number of modifications which would result in an increasedability to utilize NADH, particularly for the conversion of acetolactateto 2,3-dihydroxyisovalerate, in any KARI enzyme of interest.

In a preferred embodiment, the modified or mutated KARI enzymes havefrom 1 to 4 amino acid substitutions in amino acid regions involved incofactor specificity as compared to the wild-type KARI enzyme proteins.In other embodiments, the modified or mutated KARI enzymes haveadditional amino acid substitutions at other positions as compared tothe respective wild-type KARI enzymes. Thus, modified or mutated KARIenzymes may have at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40 different residues in other positionsas compared to the respective wild-type KARI enzymes. As will beappreciated by those of skill in the art, the number of additionalpositions that may have amino acid substitutions will depend on thewild-type KARI enzyme used to generate the variants. Thus, in someinstances, up to 50 different positions may have amino acidsubstitutions.

The nucleotide sequences for several KARI enzymes are known. Forinstance, the sequences of KARI enzymes are available from a vast arrayof microorganisms, including, but not limited to, Escherichia coli(GenBank No: NP_(—)418222), Saccharomyces cerevisiae (GenBank Nos:NP_(—)013459, Methanococcus maripaludis (GenBank No: YP_(—)001097443),Bacillus subtilis (GenBank Nos: CAB14789), and the KARI enzymes fromPiromyces sp (GenBank No: CAA76356), Buchnera aphidicola (GenBank No:AAF13807), Spinacia oleracea (GenBank Nos: Q01292 and CAA40356), Oryzasativa (GenBank No: NP_(—)001056384) Chlamydomonas reinhardtii (GenBankNo: XP_(—)001702649), Neurospora crassa (GenBank No: XP_(—)961335),Schizosaccharomyces pombe (GenBank No: NP_(—)001018845), Laccariabicolor (GenBank No: XP_(—)001880867), Ignicoccus hospitalis (GenBankNo: YP_(—)001435197), Picrophilus torridus (GenBank No: YP_(—)023851),Acidiphilium cryptum (GenBank No: YP_(—)001235669),Cyanobacteria/Synechococcus sp. (GenBank No: YP_(—)473733), Zymomonasmobilis (GenBank No: YP_(—)162876), Bacteroides thetaiotaomicron(GenBank No: NP_(—)810987), Methanococcus maripaludis (GenBank No:YP_(—)001097443), Vibrio fischeri (GenBank No: YP_(—)205911), Shewanellasp (GenBank No: YP_(—)732498), Gramella forsetti (GenBank No:YP_(—)862142), Psychromonas ingrhamaii (GenBank No: YP_(—)942294), andCytophaga hutchinsonii (GenBank No: YP_(—)677763)

Improved NADH-Dependent Activity

In one aspect, the NADH-dependent activity of the modified or mutatedKARI enzyme is increased.

In a preferred embodiment, the catalytic efficiency of the modified ormutated KARI enzyme is improved for the cofactor NADH. Preferably, thecatalytic efficiency of the modified or mutated KARI enzyme is improvedby at least about 5% as compared to the wild-type or parental KARI forNADH. More preferably the catalytic efficiency of the modified ormutated KARI enzyme is improved by at least about 15% as compared to thewild-type or parental KARI for NADH. More preferably, the catalyticefficiency of the modified or mutated KARI enzyme is improved by atleast about 25% as compared to the wild-type or parental KARI for NADH.More preferably, the catalytic efficiency of the modified or mutatedKARI enzyme is improved by at least about 50% as compared to thewild-type or parental KARI for NADH. More preferably, the catalyticefficiency of the modified or mutated KARI enzyme is improved by atleast about 75% as compared to the wild-type or parental KARI for NADH.More preferably, the catalytic efficiency of the modified or mutatedKARI enzyme is improved by at least about 100% as compared to thewild-type or parental KARI for NADH. More preferably, the catalyticefficiency of the modified or mutated KARI enzyme is improved by atleast about 300% as compared to the wild-type or parental KARI for NADH.More preferably, the catalytic efficiency of the modified or mutatedKARI enzyme is improved by at least about 500% as compared to thewild-type or parental KARI for NADH. More preferably, the catalyticefficiency of the modified or mutated KARI enzyme is improved by atleast about 1000% as compared to the wild-type or parental KARI forNADH. More preferably, the catalytic efficiency of the modified ormutated KARI enzyme is improved by at least about 5000% as compared tothe wild-type or parental KARI for NADH.

In a preferred embodiment, the catalytic efficiency of the modified ormutated KARI enzyme with NADH is increased with respect to the catalyticefficiency of the wild-type or parental enzyme with NADPH. Preferably,the catalytic efficiency of the modified or mutated KARI enzyme is atleast about 10% of the catalytic efficiency of the wild-type or parentalKARI enzyme for NADPH. More preferably, the catalytic efficiency of themodified or mutated KARI enzyme is at least about 25% of the catalyticefficiency of the wild-type or parental KARI enzyme for NADPH. Morepreferably, the catalytic efficiency of the modified or mutated KARIenzyme is at least about 50% of the catalytic efficiency of thewild-type or parental KARI enzyme for NADPH. More preferably, thecatalytic efficiency of the modified or mutated KARI enzyme is at leastabout 75%, 85%, 95% of the catalytic efficiency of the wild-type orparental KARI enzyme for NADPH.

In a preferred embodiment, the K_(M) of the KARI enzyme for NADH isdecreased relative to the wild-type or parental enzyme. A change inK_(M) is evidenced by at least a 5% or greater increase or decrease inK_(M) compared to the wild-type KARI enzyme. In certain embodiments,modified or mutated KARI enzymes of the present invention may showgreater than 10 times decreased K_(M) for NADH compared to the wild-typeor parental KARI enzyme. In certain embodiments, modified or mutatedKARI enzymes of the present invention may show greater than 30 timesdecreased K_(M) for NADH compared to the wild-type or parental KARIenzyme.

In a preferred embodiment, the k_(cat) of the KARI enzyme with NADH isincreased relative to the wild-type or parental enzyme. A change ink_(cat) is evidenced by at least a 5% or greater increase or decrease inK_(M) compared to the wild-type KARI enzyme. In certain embodiments,modified or mutated KARI enzymes of the present invention may showgreater than 50% increased k_(cat) for NADH compared to the wild-type orparental KARI enzyme. In certain embodiments, modified or mutated KARIenzymes of the present invention may show greater than 100% increasedk_(cat) for NADH compared to the wild-type or parental KARI enzyme. Incertain embodiments, modified or mutated KARI enzymes of the presentinvention may show greater than 200% increased k_(cat) for NADH comparedto the wild-type or parental KARI enzyme.

Cofactor Switch

In preferred embodiments, the cofactor specificity of the modified ormutated KARI enzyme is altered such that there is a cofactor switch fromNADPH to NADH. In other words, these modified or mutated KARI enzymeswill have an increase in NADH-dependent activity and a substantiallysimultaneous decrease in NADPH dependent activity. Thus, the methods ofthe present invention can be used to change the cofactor preference fromNADPH to NADH.

“Cofactor specificity” is a measure of the specificity of an enzyme forone cofactor over another. Thus, the methods of the present inventionmay be used to alter the cofactor preference of the target enzyme, suchthat the preference for the less favored cofactor is increased by 20%,50%, 100%, 300%, 500%, 1000%, up to 2000%. For example, a number ofreductase enzymes have been described that favor NADPH over NADH (seeWO/2002/022526; WO/2002/029019; Mittl et al., 1994, Protein Sci., 3:1504-14; Banta et al., (2002) Protein Eng., 15: 131-140; all of whichare hereby incorporated by reference in their entirety). As theavailability of NADPH is often limiting, both in vivo and in vitro, theoverall activity of the target protein is often limited. For targetproteins that prefer NADPH as a cofactor, it would be desirable to alterthe cofactor specificity of the target protein (e.g. a KARI enzyme) to acofactor that is more readily available, such as NADH.

In a preferred embodiment, the cofactor specificity of the KARI enzymeis switched. By “switched” herein is meant, that the cofactor preference(in terms of catalytic efficiency (k_(cat)/K_(M)) of the KARI enzyme ischanged to another cofactor Preferably, in one embodiment, by switchingcofactor specificity, activity in terms of catalytic efficiency(k_(cat)/K_(M)) with the cofactor preferred by the wild-type KARI enzymeis reduced, while the activity with the less preferred cofactor isincreased. This can be achieved, for example by increasing the k_(cat)for less preferred cofactor over the preferred cofactor or by decreasingK_(M) for the less preferred cofactor over the preferred cofactor orboth.

In a preferred embodiment, the KARI enzyme is modified or a mutated tobecome NADH-dependent. The term “NADH-dependent” refers to the propertyof an enzyme to preferentially use NADH as the redox cofactor. AnNADH-dependent enzyme has a higher catalytic efficiency (k_(cat)/K_(M))with the cofactor NADH than with the cofactor NADPH as determined by invitro enzyme activity assays. Accordingly, the term “NADPH-dependent”refers to the property of an enzyme to preferentially use NADPH as theredox cofactor. An NADPH dependent enzyme has a higher catalyticefficiency (k_(cat)/K_(M)) with the cofactor NADPH than with thecofactor NADH as determined by in vitro enzyme activity assays.

In a preferred embodiment, the catalytic efficiency of the KARI enzymefor NADH is enhanced relative to the catalytic efficiency with NADPH.The term “catalytic efficiency” describes the ratio of the rate constantk_(cat) over the Michaelis-Menten constant K_(M). In one embodiment, theinvention is directed to a modified or mutated KARI enzyme that exhibitsat least about a 1:10 ratio of catalytic efficiency (k_(cat)/K_(M)) withNADH over catalytic efficiency with NADPH. In another embodiment, themodified or mutated KARI enzyme exhibits at least about a 1:1 ratio ofcatalytic efficiency (k_(cat)/K_(M)) with NADH over catalytic efficiencywith NADPH. In yet another embodiment, the modified or mutated KARIenzyme exhibits at least about a 10:1 ratio of catalytic efficiency(k_(cat)/K_(M)) with NADH over catalytic efficiency with NADPH. In yetanother embodiment, the modified or mutated KARI enzyme exhibits atleast about a 100:1 ratio of catalytic efficiency (k_(cat)/K_(M)) withNADH over catalytic efficiency with NADPH. In an exemplary embodiment,the modified or mutated KARI enzyme exhibits at least about a 100:1ratio of catalytic efficiency (k_(cat)/K_(M)) with NADH over catalyticefficiency with NADPH.

In a preferred embodiment, the K_(M) of the KARI enzyme for NADH isdecreased relative to the K_(M) of the KARI enzyme for NADPH. In oneembodiment, the invention is directed to a modified or mutated KARIenzyme that exhibits at least about a 10:1 ratio of K_(M) for NADH overK_(M) for NADPH. In one embodiment, the invention is directed to amodified or mutated KARI enzyme that exhibits at least about a 1:1 ratioof K_(M) for NADH over K_(M) for NADPH. In a preferred embodiment, theinvention is directed to a modified or mutated KARI enzyme that exhibitsat least about a 1:10 ratio of K_(M) for NADH over K_(M) for NADPH. Inyet another embodiment, the invention is directed to a modified ormutated KARI enzyme that exhibits at least about a 1:20, 1:100, 1:1000ratio of K_(M) for NADH over K_(M) for NADPH.

In another preferred embodiment, the k_(cat) of the KARI enzyme withNADH is increased relative to k_(cat) with NADPH. In certainembodiments, modified or mutated KARI enzymes of the present inventionmay show greater than 0.8:1 ratio of k_(cat) with NADH over k_(cat) withNADPH. In certain embodiments, modified or mutated KARI enzymes of thepresent invention may show greater than 1:1 ratio of k_(cat) with NADHover k_(cat) with NADPH. In a preferred embodiment, modified or mutatedKARI enzymes of the present invention may show greater than 10:1 ratioof k_(cat) with NADH over k_(cat) with NADPH. In certain embodiments,modified or mutated KARI enzymes of the present invention may showgreater than 100:1 ratio of k_(cat) with NADH over k_(cat) with NADPH.

Identification of Corresponding Amino Acid Substitutions in HomologousEnzymes

An amino acid sequence alignment of 22 KARIs (including E. coli IlvC,spinach KARI and rice KARI) was described in commonly owned andco-pending applications U.S. Ser. No. 12/610,784 and PCT/US09/62952(published as WO/2010/051527). Various KARIs aligned with the E. coliKARI sequence at amino acid positions 71, 76, 78, and 110 and thisallows to conclude that the beneficial mutations found for E. coli KARIconfer the same effects in these KARI enzymes.

A structure alignment of E. coli KARI (PDB ID NO. 1YRL) with rice KARI(PDB ID NO. 3FR8) as a representative of the shorter loop group has beenperformed and the sites of useful mutations in the E. coli contextcorresponded reasonably well with specific residues in the context ofthe shorter loop: Ser165, Lys166, and Ser167. Ser165 of (correspondingto A71 in E. coli) therefore may be substituted with aspartate. A chargereversal at position K166 (corresponding to position R76D) may yield thesame result. Ser167 may correspond to Ser78 and a mutation to aspartatecorresponds to a beneficial mutation at Q110, and thus can betransferable in the aligned KARIs.

NADH-Dependent ADH Enzymes

Several alcohol dehydrogenases may be suitable candidates for conversioninto an NADH-dependent isobutyraldehyde dehydrogenase. Among theexemplary enzymes for conversion are S. cerevisiae ADH1, Zymomonasmobilis ADHII, E. coli YqhD, herein referred to as Ec_YqhD, and S.cerevisiae ADH7.

As described in WO/2008/098227, the S. cerevisiae ADH2 gene is expectedto be functionally expressed from pSA55 and required for catalyzing thefinal step of the isobutanol biosynthetic pathway, namely the conversionof isobutyraldehyde to isobutanol. Thus, no isobutanol should beproduced with the plasmid combination lacking ADH2 as adhE is deleted inJCL260. However, the results of a fermentation using a strain withoutoverexpression of any gene encoding an enzyme with ADH activity for theconversion of isobutyraldehyde to isobutanol showed that overexpressionof an ADH enzyme is not required for isobutanol production in E. coli.In fact, isobutanol production for the system lacking ADH2 was higherthan for the system with ADH2 expression. Volumetric productivity andtiter showed 42% increase, specific productivity showed 18% increase andyield 12% increase. This suggests strongly that a native E. colidehydrogenase is responsible for the conversion of isobutyraldehyde toisobutanol.

Surprisingly, this last step of the isobutanol biosynthetic pathway wasfound to be carried out by a native E. coli dehydrogenase. Approximately˜80% of the isobutyraldehyde reduction activity is due to Ec_YqhD undercertain culture conditions. Available literature on Ec_YqhD suggeststhat while it does prefer long-chain alcohols, it also utilizes NADPH(versus NADH) (Perez et al., 2008, J. Biol. Chem. 283: 7346-53).

Switching the cofactor specificity of an NADPH-dependent alcoholdehydrogenase may be complicated by the fact that cofactor bindinginduces a conformational change, resulting in an anhydrous bindingpocket that facilitates hydride transfer from the reduced cofactor tothe aldehyde (Leskovac et al., 2002, Ferns Yeast Research, 2: 481-94;Reid et al., 1994, Critical Reviews in Microbiology, 20: p. 13-56).Mutations that are beneficial for binding NADH may have deleteriouseffects with respect to this conformational change.

Alternatively, isobutyraldehyde reduction activity of an NADH-dependentenzyme with little native activity towards this substrate may beincreased. This approach has the advantages that (1) several specializedenzymes exist in nature that are highly active under fermentativeconditions, (2) the binding sites of several of these enzymes are known,(3) mutational studies indicate that substrate specificity can easily bealtered to achieve high activity on a new substrate.

Several alcohol dehydrogenase enzymes may be suitable candidates forconversion into an NADH-dependent isobutyraldehyde dehydrogenase: S.cerevisiae ADH1 and Zymomonas mobilis ADHII are NADH-dependent enzymesresponsible for the conversion of acetaldehyde to ethanol underanaerobic conditions. These enzymes are highly active. The substratespecificity for these enzymes has been analyzed (Leskovac et al., 2002,Ferns Yeast Research, 2: 481-94; Rellos et al., 1997, Protein Expressionand Purification, 9: 89-90), the amino acid residues comprising thesubstrate binding pocket are known (Leskovac et al., 2002, Ferns YeastResearch, 2: 481-94; Rellos et al., 1997, Protein Expression andPurification, 9: 89-90), and attempts to alter the substrate specificityby mutation have revealed that the substrate specificity can be altered(Rellos et al., 1997, Protein Expression and Purification, 9: 89-90;Green et al., 1993, J. Biol. Chem., 268: 7792-98). Ec_YqhD and S.cerevisiae ADH7 are NADPH-dependent enzymes whose physiologicalfunctions are not as well understood. Ec_YqhD has been implicated in theprotection of the cell from peroxide-derived aldehydes (Perez et al.,2008, J. Biol. Chem. 283: 7346-53). The substrate specificity of bothenzymes is understood, and amino acids lining the substrate bindingpocket are known (Perez et al., 2008, J. Biol. Chem. 283: 7346-53).Based on the known amino acid residues implicated in substrate binding(S. cerevisiae ADH1, Z. mobilis ADHII) or the cofactor binding site(Ec_yqhD), sites with the highest likelihood of affecting desired enzymefeatures such as substrate specificity or cofactor specificity may bemutated to generate the desired function.

One approach to increase activity of enzymes with NADH as the cofactoris saturation mutagenesis with NNK libraries at each of the residuesthat interact with the cofactor. These libraries can be screened foractivity in the presence of NADPH and NADH in order to identify whichsingle mutations contribute to increased activity on NADH and alteredspecificity for NADH over NADPH. Combinations of mutations ataforementioned residues can be investigated by any method known in theart. For example, a combinatorial library of mutants may be designedbased on the results of the saturation mutagenesis studies. For example,a combinatorial library of mutants may be designed including only thosemutations that do not lead to decrease in NADH-dependent activity.

Another approach to increase the NADH-dependent activity of the enzymeis to perform saturation mutagenesis of a first amino acid thatinteracts with the cofactor, then isolate the mutant with the highestactivity using NADH as the cofactor, then perform saturation mutagenesisof a second amino acid that interacts with the cofactor, and so on.Similarly, a limited number of amino acids that interact with thecofactor may be targeted for randomization simultaneously and then bescreened for improved activity with NADH as the cofactor. The selected,best mutant can then be subjected to the same procedure again and thisapproach may be repeated iteratively until the desired result isachieved.

Another approach is to use random oligonucleotide mutagenesis togenerate diversity by incorporating random mutations, encoded on asynthetic oligonucleotide, into the cofactor binding region of theenzyme. The number of mutations in individual enzymes within thepopulation may be controlled by varying the length of the targetsequence and the degree of randomization during synthesis of theoligonucleotides. The advantages of this more defined approach are thatall possible amino acid mutations and also coupled mutations can befound.

If the best variants from the experiments described above are notsufficiently active with NADH as the cofactor, directed evolution viaerror-prone PCR may be used to obtain further improvements. Error-pronePCR mutagenesis of the first domain containing the cofactor bindingpocket may be performed followed by screening for ADH activity with NADHand/or increased specificity for NADH over NADPH as the cofactor.

Surprisingly, alcohol dehydrogenase enzymes that are not known tocatalyze the reduction of isobutyraldehyde to isobutanol were identifiedthat catalyze this reaction. Thus, in another aspect, such an alcoholdehydrogenase may be encoded by an NADH-dependent 1,3-propanedioldehydrogenase. In yet another aspect, such an alcohol dehydrogenase maybe encoded by an NADH-dependent 1,2-propanediol dehydrogenase. Preferredenzymes of this disclosure include enzymes listed in Table 1 ofco-pending and commonly owned U.S. Ser. No. 12/610,784 andPCT/US09/62952 (published as WO/2010/051527). These enzymes exhibitNADH-dependent isobutyraldehyde reduction activity, measured as Unit perminute per mg of crude cell lysate (U min⁻¹ mg⁻¹) that is approximatelysix-fold to seven-fold greater than the corresponding NADPH-dependentisobutyraldehyde reduction activity.

In addition to exhibiting increased activity with NADH as the cofactoras compared to the NADPH, alcohol dehydrogenases of the presentinvention may further be more active as compared to the native E. colialcohol dehydrogenase Ec_YqhD. In particular, alcohol dehydrogenases ofthe present invention may exhibit increased activity and/or decreasedK_(M) values with NADH as the cofactor as compared to Ec_YqhD with NADPHas the cofactor. Exemplary enzymes that exhibit greater NADH-dependentalcohol dehydrogenase activity than the NADPH-dependent alcoholdehydrogenase activity are listed include the Drosophila melanogasterADH, the L. lactis adhA, K. pneumoniae dhaT, and E. coli fucO (see Table1 of U.S. Ser. No. 12/610,784).

Alcohol dehydrogenases of the present disclosure may also be utilized inmetabolically-modified microorganisms that include recombinantbiochemical pathways useful for producing additional alcohols such as2-methyl-1-butanol, 3-methyl-1-butanol, 2-phenylethanol, 1-propanol, or1-butanol via conversion of a suitable substrate by a modifiedmicroorganism.

Microorganisms producing such compounds have been described(WO/2008/098227). For example, these alcohols can be 1-propanol,1-butanol, 2-methyl-1-butanol, 3-methyl-1-butanol or 2-phenylethanol andare generally produced from a metabolite comprising a 2-keto acid. Insome aspects, the 2-keto acid includes 2-ketobutyrate, 2-ketovalerate,2-keto-3-methylvalerate, 2-keto-4-methyl-pentanoate, or phenylpyruvate.The 2-ketoacid is converted to the respective aldehyde by a 2-ketoaciddecarboxylase. For example, 2-ketobutyrate is converted to 1-propanal,2-ketovalerate is converted to 1-butanal, 2-keto-3-methylvalerate isconverted to 2-methyl-1-butanol, 2-keto-4-methyl-pentanoate is convertedto 3-methyl-1-butanal, and phenylpyruvate is converted to phenylethanalby a 2-ketoacid decarboxylase. Thus, the recombinant microorganismincludes elevated expression or activity of a 2-keto-acid decarboxylase,as compared to a parental microorganism. The 2-keto-acid decarboxylasemay be encoded by kivD from Lactococcus lactis, or homologs thereof. The2-keto-acid decarboxylase can be encoded by a polynucleotide derivedfrom a gene selected from kivD from L. lactis, or homologs thereof.

In earlier publications (See, e.g., WO/2008/098227), onlyNADPH-dependent alcohol dehydrogenases are described that convert theaforementioned aldehyde to an alcohol. In particular, S. cerevisiaeAdh2p is described that converts the aldehyde to the respectivealdehyde.

Thus, in one embodiment of this disclosure, a microorganism is providedin which the cofactor dependent final step for the conversion of thealdehyde to the respective alcohol is catalyzed by an NADH-dependentalcohol dehydrogenase. In particular, NADH-dependent alcoholdehydrogenases are disclosed that catalyze the reduction aldehydes toalcohols, for example, of 1-propanal to 1-propanol, 1-butanal to1-butanol, 2-methyl-1-butanal to 2-methyl-1-butanol, 3-methyl-1-butanalto 3-methyl-1-butanol, or phenylethanal to phenylethanol.

In a specific aspect, such an alcohol dehydrogenase may be encoded bythe Drosophila melanogaster alcohol dehydrogenase Dm_Adh or homologsthereof. In another specific aspect, such an alcohol dehydrogenase maybe encoded by the Lactococcus lactis alcohol dehydrogenase (LI_AdhA) orhomologs thereof.

Surprisingly, alcohol dehydrogenase enzymes that are not known tocatalyze the reduction of isobutyraldehyde to isobutanol were identifiedthat catalyze this reaction. Thus, in another aspect, such an alcoholdehydrogenase may be encoded by an NADH-dependent 1,3-propanedioldehydrogenase. In yet another aspect, such an alcohol dehydrogenase maybe encoded by an NADH-dependent 1,2-propanediol dehydrogenase.

In another embodiment, a method of producing an alcohol is provided. Themethod includes providing a recombinant microorganism provided herein;culturing the microorganism of in the presence of a suitable substrateor metabolic intermediate and under conditions suitable for theconversion of the substrate to an alcohol; and detecting the productionof the alcohol. In various aspects, the alcohol is selected from1-propanol, 1-butanol, 2-methyl 1-butanol, 3-methyl 1-butanol, and2-phenylethanol. In another aspect, the substrate or metabolicintermediate includes a 2-keto acid-derived aldehyde, such as1-propanal, 1-butanal, 2-methyl-1-butanal, 3-methyl-1-butanal, orphenylethanal.

Recombinant Host Cells Comprising a NADH-Dependent KARI and/or ADHEnzymes

In an additional aspect, the present invention is directed torecombinant host cells (i.e. metabolically “engineered” or “modified”microorganisms) comprising NADH-dependent KARI and/or ADH enzymes of theinvention. Recombinant microorganisms provided herein can express aplurality of additional heterologous and/or native target enzymesinvolved in pathways for the production of beneficial metabolites suchas isobutanol from a suitable carbon source.

Accordingly, metabolically “engineered” or “modified” microorganisms areproduced via the introduction of genetic material (i.e. a NADH-dependentKARI and/or ADH enzymes) into a host or parental microorganism ofchoice, thereby modifying or altering the cellular physiology andbiochemistry of the microorganism. Through the introduction of geneticmaterial and/or the modification of the expression of native genes theparental microorganism acquires new properties, e.g. the ability toproduce a new, or greater quantities of, an intracellular metabolite. Asdescribed herein, the introduction of genetic material and/or themodification of the expression of native genes into a parentalmicroorganism results in a new or modified ability to produce beneficialmetabolites such as isobutanol. The genetic material introduced intoand/or the genes modified for expression in the parental microorganismcontains gene(s), or parts of genes, coding for one or more of theenzymes involved in a biosynthetic pathway for the production ofisobutanol and may also include additional elements for the expressionand/or regulation of expression of these genes, e.g. promoter sequences.

Recombinant microorganisms provided herein may also produce metabolitesin quantities not available in the parental microorganism. A“metabolite” refers to any substance produced by metabolism or asubstance necessary for or taking part in a particular metabolicprocess. A metabolite can be an organic compound that is a startingmaterial (e.g., glucose or pyruvate), an intermediate (e.g.,2-ketoisovalerate), or an end product (e.g., 1-propanol, 1-butanol,isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol) of metabolism.Metabolites can be used to construct more complex molecules, or they canbe broken down into simpler ones. Intermediate metabolites may besynthesized from other metabolites, perhaps used to make more complexsubstances, or broken down into simpler compounds, often with therelease of chemical energy.

Exemplary metabolites include glucose, pyruvate, 1-propanol, 1-butanol,isobutanol, 2-methyl-1-butanol, and 3-methyl-1-butanol.

The metabolite 1-propanol can be produced by a recombinant microorganismengineered to express or over-express a metabolic pathway that convertspyruvate to 1-propanol. An exemplary metabolic pathway that convertspyruvate to 1-propanol has been described in WO/2008/098227 and byAtsumi et al. (Atsumi et al., 2008, Nature 451(7174): 86-9), thedisclosures of which are herein incorporated by reference in theirentireties. In a preferred embodiment, metabolic pathway comprises aKARI and/or an ADH enzyme of the present invention.

The metabolite 1-butanol can be produced by a recombinant microorganismengineered to express or over-express a metabolic pathway that convertspyruvate to 3-methyl-1-butanol. An exemplary metabolic pathway thatconverts pyruvate to 3-methyl-1-butanol has been described inWO/2008/098227 and by Atsumi et al. (Atsumi et al., 2008, Nature451(7174): 86-9), the disclosures of which are herein incorporated byreference in their entireties. In a preferred embodiment, metabolicpathway comprises a KARI and/or an ADH enzyme of the present invention.

The metabolite isobutanol can be produced by a recombinant microorganismengineered to express or over-express a metabolic pathway that convertspyruvate to isobutanol. An exemplary metabolic pathway that convertspyruvate to isobutanol may be comprised of a acetohydroxy acid synthase(ALS) enzyme encoded by, for example, alsS from B. subtilis, a ketolacidreductoisomerase (KARI) of the present invention, a dihydroxy-aciddehydratase (DHAD), encoded by, for example ilvD from E. coli or L.lactis, a 2-keto-acid decarboxylase (KIVD) encoded by, for example kivdfrom L. lactis, and an alcohol dehydrogenase (ADH) of the presentinvention.

The metabolite 3-methyl-1-butanol can be produced by a recombinantmicroorganism engineered to express or over-express a metabolic pathwaythat converts pyruvate to 3-methyl-1-butanol. An exemplary metabolicpathway that converts pyruvate to 3-methyl-1-butanol has been describedin WO/2008/098227 and by Atsumi et al. (Atsumi et al., 2008, Nature451(7174): 86-9), the disclosures of which are herein incorporated byreference in their entireties. In a preferred embodiment, metabolicpathway comprises a KARI and/or an ADH enzyme of the present invention.

The metabolite 2-methyl-1-butanol can be produced by a recombinantmicroorganism engineered to express or over-express a metabolic pathwaythat converts pyruvate to 2-methyl-1-butanol. An exemplary metabolicpathway that converts pyruvate to 2-methyl-1-butanol has been describedin WO/2008/098227 and by Atsumi et al. (Atsumi et al., 2008, Nature 451:86-9), the disclosures of which are herein incorporated by reference intheir entireties. In an exemplary embodiment, metabolic pathwaycomprises a KARI and/or an ADH enzyme of the present invention.

The disclosure identifies specific genes useful in the methods,compositions and organisms of the disclosure; however it will berecognized that absolute identity to such genes is not necessary. Forexample, changes in a particular gene or polynucleotide comprising asequence encoding a polypeptide or enzyme can be performed and screenedfor activity. Typically such changes comprise conservative mutation andsilent mutations. Such modified or mutated polynucleotides andpolypeptides can be screened for expression of a functional enzyme usingmethods known in the art. In addition, homologs of enzymes useful forgenerating metabolites are encompassed by the microorganisms and methodsprovided herein.

Microorganism Characterized by Increased Capacity to ProduceIntermediates of the Isobutanol Pathway

As a consequence of increased yield of isobutanol, it follows that thisyeast microorganism exhibits a higher capacity to produce theintermediates of the isobutanol pathway including, but not limited to,acetolactate, 2,3-dihydroxyisovalerate, keto-isovalerate, andisobutyraldehyde.

Method of Using Microorganism for High-Yield Isobutanol Fermentation

In a method to produce isobutanol from a carbon source at high yield,the yeast microorganism is cultured in an appropriate culture mediumcontaining a carbon source.

Another exemplary embodiment provides a method for producing isobutanolcomprising a recombinant yeast microorganism of the invention in asuitable culture medium containing a carbon source that can be convertedto isobutanol by the yeast microorganism of the invention.

In certain embodiments, the method further includes isolating isobutanolfrom the culture medium. For example, isobutanol may be isolated fromthe culture medium by any method known to those skilled in the art, suchas distillation, pervaporation, or liquid-liquid extraction.

EXAMPLES General Methods

Sample preparation: Samples (2 mL) from the fermentation broth werestored at −20° C. for later substrate and product analysis. Prior toanalysis, samples were thawed and then centrifuged at 14,000×g for 10min. The supernatant was filtered through a 0.2 μm filter. Analysis ofsubstrates and products was performed using authentic standards (>99%,obtained from Sigma-Aldrich), and a 5-point calibration curve (with1-pentanol as an internal standard for analysis by gas chromatography).

Determination of optical density and cell dry weight: The opticaldensity of the yeast cultures was determined at 600 nm using a DU 800spectrophotometer (Beckman-Coulter, Fullerton, Calif., USA). Sampleswere diluted as necessary to yield an optical density of between 0.1 and0.8. The cell dry weight was determined by centrifuging 50 mL of cultureprior to decanting the supernatant. The cell pellet was washed once with50 mL of milliQ H₂O, centrifuged and the pellet was washed again with 25mL of milliQ H₂O. The cell pellet was then dried at 80° C. for at least72 hours. The cell dry weight was calculated by subtracting the weightof the centrifuge tube from the weight of the centrifuge tube containingthe dried cell pellet.

Gas Chromatography: Analysis of ethanol and isobutanol was performed ona HP 5890 gas chromatograph fitted with a DB-FFAP column (AgilentTechnologies; 30 m length, 0.32 mm ID, 0.25 μM film thickness) orequivalent connected to a flame ionization detector (FID). Thetemperature program was as follows: 200° C. for the injector, 300° C.for the detector, 100° C. oven for 1 minute, 70° C./minute gradient to235° C., and then hold for 2.5 min.

High Performance Liquid Chromatography: Analysis of glucose and organicacids was performed on a HP-1100 High Performance Liquid Chromatographysystem equipped with an Aminex HPX-87H Ion Exclusion column (Bio-Rad,300×7.8 mm) or equivalent and an cation guard column (Bio-Rad) orequivalent. Organic acids were detected using an HP-1100 UV detector(210 nm, 8 nm 360 nm reference) while glucose was detected using anHP-1100 refractive index detector. The column temperature was 60° C.This method was Isocratic with 0.008N sulfuric acid in water as mobilephase. Flow was set at 0.6 mL/min. Injection size was 20 μL and the runtime was 30 minutes.

Anaerobic batch fermentations: Anaerobic batch cultivations wereperformed at 30° C. in stoppered 100 mL serum bottles. A total of 20 mLof synthetic medium with an initial glucose concentration of 20g-glucose L⁻¹ was used (Kaiser et al., Methods in Yeast Genetics, a ColdSpring Harbor Laboratory Manual (1994)). 2 mL samples are taken at 24and 48 hours. The fermentation is ended after 48 hours or when allglucose is consumed. Samples are processed and analyzed by GasChromatography and/or High Performance Liquid Chromatography asdescribed above.

Yeast transformations—K. lactis: Transformations were performed byelectroporation according to Kooistra et al., Yeast 21:781-792 (2004).

Lithium Acetate transformations of S. cerevisiae strains weretransformed by the Lithium Acetate method (Gietz et al., Nucleic AcidsRes. 27:69-74 (1992). Cells were collected from overnight cultures grownin 50 mL of defined (SC) ethanol media at an OD₆₀₀ of approximately 0.8to 1.0 by centrifugation at 2700 rcf for 2 minutes at room temperature.The cell pellet was resuspended in 50 mL sterile water, collected bycentrifugation (2700 rcf; 2 min; room temp.), and resuspended in 25 mLsterile water. The cells were collected by centrifugation (2700 rcf; 2min; room temp.) and resuspended in 1 mL 100 mM lithium acetate. Thecell suspension was transferred to a sterile 1.5 mL tube and collectedby centrifugation at full speed for 10 seconds. The cells wereresuspended in 100 mM lithium acetate with a volume four times thevolume of the cell pellet (e.g. 400 μL for 100 μL cell pellet). To theprepared DNA Mix (72 μl 50% PEG, 10 μl 1M Lithium Acetate, 3 μl boiledsalmon sperm DNA, and 5 μl of each plasmid), 15 μl of the cellsuspension was added and mixed by vortexing with five short pulses. Thecell/DNA suspensions were incubated at 30° C. for 30 minutes and at 42°C. for 22 minutes. The cells were collected by centrifugation for 10seconds at full speed and resuspended in 100 μl SOS (1M Sorbitol, 0.34%(w/v) Yeast Extract, 0.68% (w/v) Peptone, 6.5 mM CaCl). The cellsuspensions were top spread over appropriate selective agar plates.

Yeast colony PCR: Yeast cells were taken from agar medium andtransferred to 30 μl 0.2% SDS and heated for 4 mins at 90° C. The cellswere spun down and 1 μl of the supernatant was used for PCR usingstandard Tag (NEB).

Molecular biology: Standard molecular biology methods for cloning andplasmid construction were generally used, unless otherwise noted(Sambrook & Russell).

Media:

YP: contains 1% (w/v) yeast extract, 2% (w/v) peptone. YPD is YPcontaining 2% (w/v) glucose, YPE is YP containing 2% (w/v) Ethanol.

SC+Complete: 20 g/L glucose, 14g/L Sigma™ Synthetic Dropout Mediasupplement (includes amino acids and nutrients excluding histidine,tryptophan, uracil, and leucine), and 6.7 g/L Difco™ Yeast NitrogenBase. 0.076 g/L histidine, 0.076 g/L tryptophan, 0.380 g/L leucine, and0.076 g/L uracil.

SC-HWUL: 20 g/L glucose, 14 g/L Sigma™ Synthetic Dropout Mediasupplement (includes amino acids and nutrients excluding histidine,tryptophan, uracil, and leucine), and 6.7 g/L Difco™ Yeast Nitrogen Base

SC-WLU: 20 g/L glucose, 14 g/L Sigma™ Synthetic Dropout Media supplement(includes amino acids and nutrients excluding histidine, tryptophan,uracil, and leucine), 6.7 g/L Difco™ Yeast Nitrogen Base without aminoacids, and 0.076 g/L histidine.

SC- HWU: 20 g/L glucose, 14 g/L Sigma™ Synthetic Dropout Mediasupplement (includes amino acids and nutrients excluding histidine,tryptophan, uracil, and leucine), 6.7 g/L Difco™ Yeast Nitrogen Basewithout amino acids, and 0.380 g/L leucine.

SC-Ethanol-HWU: 2% (w/v) ethanol, 14 g/L Sigma™ Synthetic Dropout Mediasupplement (includes amino acids and nutrients excluding histidine,tryptophan, uracil, and leucine), 6.7 g/L Difco™ Yeast Nitrogen Base,and 0.380 g/L leucine.

Solid versions of the above described media contain 2% (w/v) agar.

Strains, Plasmids and Primer Sequences

Table 1 details the genotype of strains disclosed herein:

GEVO No. Genotype and/or Reference GEVO1187 S. cerevisiae CEN.PK MAT aho his3- leu2 trp1 ura3 PDC1 PDC5 PDC6 GEVO1188 S. cerevisiae CEN.PK MATalpha ho his3- leu2 trp1 ura3 PDC1 PDC5 PDC6 GEVO1287¹ K. lactis MATαuraA1 trp1 leur2 lysA1 ade1 lac4-8 [pKD1] (ATCC #87365) GEVO1537² S.cerevisiae HO/HO pdc1::Tn5ble/pdc1::Tn5ble pdc5::Tn5ble/pdc5::Tn5blepdc6::APT1/pdc6::APT1 HIS3/HIS, LEU2/LEU2, URA3/URA3, TRP1/TRP1 Gevo1538S. cerevisiae MAT a/α, HIS3, LEU2, TRP1, URA3, pdc1::ble/pdc1::ble,pdc5::ble/pdc5::ble, pdc6::apt1(kanR)/pdc6::apt1(kanR), HO/HO GEVO1581S. cerevisiae MAT a/alpha, his3/his3, trp1/trp1, ura3/ura3, LEU2/LEU2,pdc1::ble/pdc1::ble, pdc5::ble/pdc5::ble,pdc6::apt1(kanR)/pdc6::apt1(kanR), HO/HO Gevo1715 S. cerevisiae MAT a,leu2, ura3, pdc1::ble, pdc5::ble, pdc6::apt1(kanR), ho GEVO1584 S.cerevisiae MAT a, his3, trp1, ura3, leu2, pdc1::ble, pdc5::ble,pdc6::apt1(kanR), ho- GEVO1742 K. lactis MATα uraA1 trp1 leur2 lysA1ade1 lac4-8 [pKD1] Klpdc1Δ::pGV1537 (G418^(R))] GEVO1794 K. lactisMATalpha uraA1 trp1 leu2 lysA1 ade1 lac4-8 [pKD1] pdc1::kan {Ll-kivd;Sc- Adh7:KmURA3 integrated} GEVO1818 K. lactis MATalpha uraA1 trp1 leu2lysA1 ade1 lac4-8 [pKD1] pdc1::kan {Ec-ilvC- deltaN;Ec-ilvD-deltaN(codon opt for K. lactis): Sc-LEU2 integrated} {Ll-kivd;Sc- Adh7: KmURA3 integrated} GEVO1829 K. lactis MATalpha uraA1 trp1 leu2lysA1 ade1 lac4-8 [pKD1] pdc1::kan {Ec-ilvC- deltaN;Ec-ilvD-deltaN(codon opt for K. lactis): Sc-LEU2 integrated} {Ll-kivd;Sc- Adh7: KmURA3 integrated} {ScCUP1-1 promoter: Bs alsS, TRP1 randomintegrated} Gevo1863 S. cerevisiae MAT a, his3, trp1, ura3, leu2,pdc1::ble, pdc5::ble, pdc6::apt1(kanR), ho-, chemostat-evolved to beC2-independent. ¹same as ATCC200826 ²The strains Gevo1537 and Gevo1538were originally designated GG570 (derived from strain T2-3D)and wasobtained from Paul van Heusden from the University of Leiden, theNetherlands. For complete references for both strains, see: Flikweert,M. T. et al., (1996) Yeast 12: 247-257.

Table 2 outlines the plasmids disclosed herein:

GEVO No. FIG. Genotype or Reference pGV1056 23 bla(amp^(r)) S.c. TDH3promoter - polylinker- CYC1 terminator CEN6/ARSH4 HIS3 pUC ori pGV106224 bla(amp^(r)) S.c. TDH3 promoter - polylinker - CYC1 terminatorCEN6/ARSH4 URA3 pUC ori pGV1102 25 bla(amp^(r)) S.c. TEF1 promoter - HAtag - polylinker- CYC1 terminator 2micron URA3 pUC ori pGV1103 26bla(amp^(r)) S.c. TDH3 promoter - myc tag - polylinker - CYC1 terminator2micron HIS3 pUC ori pGV1104 27 bla(amp^(r)) S.c. TDH3 promoter - myctag - polylinker - CYC1 terminator 2micron TRP1 pUC ori pGV1106 28bla(amp^(r)) S.c. TDH3 promoter - myc tag - polylinker - CYC1 terminator2micron URA3 pUC ori pGV1254 16 bla(amp^(r)) S.c. TEF1 promoter -HA-L.I. KIVD - S.c. TDH3 promoter - myc-S.c. ADH2 - CYC1 terminator2micron URA3 pUC ori pGV1295 17 bla(amp^(r)) S.c. TDH3 promoter -myc-ilvC - CYC1 terminator 2micron TRP1 pUC ori pGV1390 18 bla(amp^(r))S.c. CUP1-1 promoter - L.I. alsS-CYC1 terminator 2micron HIS3 pUC oripGV1438 19 bla(amp^(r)) S.c. TDH3 promoter - myc-ilvD- CYC1 terminator 2micron LEU2 pUC ori pGV1503 8 bla(amp^(r)) S.c. TEF1 promoter - KanR pUCori pGV1537 9 bla(amp^(r)) S.c. TEF1 promoter - KanR pUC ori K. lactisPDC1 5′ region - PmlI - K. lactis PDC1 3′ region pGV1429 10 bla(amp^(r))S.c. TDH3 promoter - myc tag - polylinker - CYC1 terminator 1.6micronTRP1 pUC ori pGV1430 11 bla(amp^(r)) S.c. TDH3 promoter - myc tag -polylinker - CYC1 terminator 1.6micron LEU2 pUC ori pGV1431 12bla(amp^(r)) S.c. TDH3 promoter - myc tag - polylinker - CYC1 terminator1.6micron K.m. URA3 pUC ori pGV1472 13 bla(amp^(r)) S.c. TEF1 promoter -AU1(x2)-L.I. alsS - CYC1 terminator 1.6micron LEU2 pUC ori pGV1473 14bla(amp^(r)) S.c. TEF1 promoter - AU1(x2)-E.c. ilvD - S.c. TDH3promoter - myc-E.c. ilvC - CYC1 terminator 1.6micron TRP1 pUC oripGV1475 15 bla(amp^(r)) S.c. TEF1 promoter - HA-L.I. KIVD - S.c. TDH3promoter - myc-S.c. ADH7 - CYC1 terminator 1.6micron K.m. URA3 pUC oripGV1590 20 bla(amp^(r)) S.c. TEF1 promoter - L.I. KIVD - S.c. TDH3promoter - S.c. ADH7 - CYC1 terminator 1.6micron K.m. URA3 pUC oripGV1726 21 bla(amp^(r)) S.c. CUP1-1 promoter - B.s. alsS - CYC1terminator TRP1 pUC ori pGV1727 22 bla(amp^(r)) S.c. TEF1 promoter -E.c. ilvD deltaN- S.c. TDH3 promoter -E.c. ilvC deltaN- CYC1 terminatorLEU2 pUC ori pGV1649 29 bla(amp^(r)) S.c. CUP1-1 promoter - B.s.alsS-CYC1 terminator 2micron TRP1 pUC ori pGV1664 30 bla(amp^(r)) S.c.TEF1 promoter - L.I. KIVD - S.c. TDH3 promoter - S.c. ADH7 - CYC1terminator 2micron URA3 pUC ori pGV1672 31 bla(amp^(r)) S.c. CUP1-1promoter - polylinker - CYC1 terminator CEN6/ARSH4 TRP1 pUC ori pGV167332 bla(amp^(r)) S.c. CUP1-1 promoter - B.s. alsS - CYC1 terminatorCEN6/ARSH4 TRP1 pUC ori pGV1677 33 bla(amp^(r)) S.c. TEF1 promoter -E.c. ilvD deltaN- S.c. TDH3 promoter -E.c. ilvC deltaN- CYC1 terminator2micron HIS3 pUC ori pGV1679 34 bla(amp^(r)) S.c. TEF1 promoter - E.c.ilvD deltaN- S.c. TDH3 promoter -E.c. ilvC deltaN- CYC1 terminatorCEN6/ARSH4 HIS3 pUC ori pGV1683 35 bla(amp^(r)) S.c. TEF1 promoter -L.I. KIVD - S.c. TDH3 promoter - S.c. ADH7 - CYC1 terminator CEN6/ARSH4URA3 pUC ori

Table 3 outlines the primers sequences disclosed herein:

SEQ  ID  No. Name NO: Sequence 489 MAT common 30 AGTCACATCAAGATCGTTTATGG490 MAT alpha 31 GCACGGAATATGGGACTACTTCG 491 MAT a 32ACTCCACTTCAAGTAAGAGTTTG 838 pGV1423-seq1 (838) 33 TATTGTCTCATGAGCGGATAC965 KlPDC1 −616 FOR 34 ACAACGAGTGTCATGGGGAGAGGAAGAGG 966KlPDC1 +2528 REV 35 GATCTTCGGCTGGGTCATGTGAGGCGG 995 KlPDC1 internal 36ACGCTGAACACGTTGGTGTCTTGC 996 KlPDC1 internal 37 AACCCTTAGCAGCATCGGCAACC1010 Kl-PDC1-prom-seq-c 38 TATTCATGGGCCAATACTACG 1006 Kl-PDC1-prom-3c 39GTAGAAGACGTCACCTGGTAGACCAAAGATG 1009 Kl-PDC1-term-5c 40CATCGTGACGTCGCTCAATTGACTGCTGCTA C 1016 Kl-PDC1-prom-5-v2 41ACTAAGCGACACGTGCGGTTTCTGTGGTATA (1016) G 1017 Kl-PDC1-term-3c-v2 42GAAACCGCACGTGTCGCTTAGTTTACATTTCT (1017) TTCC 1019 TEF1prom-5c (1019) 43TTTGAAGTGGTACGGCGATG 1321 Bs-alsS-Q-A5 (1321) 44 AATCATATCGAACACGATGC1324 Bs-alsS-Q-B3 (1324) 45 AGCTGGTCTGGTGATTCTAC 1325Ec-ilvC-dN-Q-A5 (1325) 46 TATCACCGTAGTGATGGTTG 1328Ec-ilvC-dN-Q-B3 (1328) 47 GTCAGCAGTTTCTTATCATCG 1330Ec-ilvD-dN-co-Kl-Q-A3 48 GCGAAACTTACTTGACGTTC (1330) 1331Ec-ilvD-dN-co-Kl-Q-B5 49 ACTTTGGACGATGATAGAGC (1331) 1334Ll-kivd-co-Ec-Q-A3 (1334) 50 GCGTTAGATGGTACGAAATC 1335Ll-kivd-co-Ec-Q-B5 (1335) 51 CTTCTAACACTAGCGACCAG 1338Sc-ADH7-Q-A3 (1338) 52 AAAGATGATGAGCAAACGAC 1339 Sc-ADH7-Q-B5 (1339) 53CGAGCAATACTGTACCAATG 1375 HO +1300 F 54 TCACGGATGATTTCCAGGGT 1376HO +1761 R 55 CACCTGCGTTGTTACCACAA

Example 1 Construction and Confirmation of PDC Deletion in K. lactis

The purpose of this Example is to describe how a PDC-deletion variant ofa member of the Saccharomyces clade, Crabtree-negative yeast, pre-WGDyeast K. lactis was constructed and confirmed.

Construction of plasmid pGV1537: Plasmid pGV1537 (SEQ ID NO: 1) wasconstructed by the following series of steps. All PCR reactions carriedout to generate pGV1537 used KOD polymerase (Novagen, Inc., Gibbstown,N.J.) and standard reaction conditions according to the manufacturer. Afirst round of two PCR reactions was carried out, wherein one PCRreaction contained primers 1006 and 1016 and used approximately 100 ngof genomic DNA from K. lactis strain GEV01287 as a template. The otherfirst-round PCR reaction contained primers 1017 and 1009 andapproximately 10Ong of genomic DNA from K. lactis strain GEVO1287 as atemplate. The two resulting PCR products (approximately 530 bp and 630bp in size, respectively) were gel purified using a Zymo Research GelDNA Extraction kit (Zymo Research, Orange, Calif.) according tomanufacturer's instructions and eluted into 10 μL of water. Two (2)microliters of each eluted PCR product were then used as a template fora final round of KOD polymerase-catalyzed PCR, which also includedprimers 1006 plus 1009. The resulting product was purified (ZymoResearch DNA Clean & Concentrate kit, Zymo Research, Orange, Calif.),digested to completion with the enzymes Mfel and Aatll, and theresulting product gel purified and eluted as described above. This DNAwas ligated into the vector pGV1503 (FIG. 8), which had been digestedwith EcoRI plus AatII, treated with calf alkaline phosphatase, and gelpurified as described above. Colonies arising from transformation of theligated DNA were screened by restriction digest analysis and confirmedby DNA sequencing reactions using primers 838, 1010, and 1019. Correctrecombinant DNA resulting from the ligation and subsequent analysis wasnamed pGV1537 (FIG. 9).

Construction of a K. lactis Klpd1Δ strain: Strain GEVO1287 wastransformed with PmlI-digested, linearized plasmid pGV1537.Transformation was carried out by electroporation with approximately 300ng of linearized pGV1537, essentially as described by Kooistra et al.(Kooistra, R., Hooykaas, P. J. J., and Steensman, H. Y. (2004)“Efficient gene targeting in Kluyveromyces lactis”. Yeast 21:781-792).Transformed cells were selected by plating onto YPD plates containing0.2 mg/mL geneticin (G418). Colonies arising from the transformationwere further selected by patching colonies onto YPD plates and thenreplica plating onto YPD containing 5 μM (final concentration) of therespiratory inhibitor Antimycin A, as Pdc-variants of K.lactis areunable to grow on glucose in the presence of Antimycin A (Bianchi, M.,et al., (1996). “The petite negative yeast Kluyveromyces lactis has asingle gene expressing pyruvate decarboxylase activity”. MolecularMicrobiology 19(1):27-36) and can therefore be identified by thismethod. Of the 83 G418-resistant colonies patched onto YPD+Antimycin A,six colonies (˜7%) were unable to grow and were therefore identified ascandidate Klpdc1::pGV1537 disruption strains.

Confirmation of a K. lactis Klpdc1Δ strain by colony PCR: CandidateKlpdc1::pGV1537 disruption strains were confirmed by colony PCRanalysis. To do so, genomic DNA from candidate lines was obtained by thefollowing method. A small amount (equivalent to a matchhead) of yeastcells were resuspended in 50 μL of 0.2% SDS and heated to 95° C. for 6minutes. The suspension was pelleted by centrifugation (30 sec,16,000×g) and 1 μL of the supernatant was used as template in 50 μL PCRreactions. In addition to standard components, the reactions containedTriton X-100 at a final concentration of 1.5% and DMSO at a finalconcentration of 5%. The various primer sets used, and the expectedamplicon sizes expected, are indicated in Table EX1-1. By theseanalyses, a correct Klpdc1Δ::pGV1537 strain was identified and was namedGEVO1742.

TABLE EX1-1 Primer pairs and expected amplicon sizes predicted forcolony PCR screening of candidate Klpdc1Δ::pGV1537 cells. Expectedproduct size for Expected product size Primer Pair Klpdc1Δ::pGV1537 forKIPDC1+ 965 & 838 796 bp (none) 1019 & 966 947 bp (none) 995 & 996(none) 765 bp

Confirmation of GEVO1742 Klpdc1Δ::pGV1537 by fermentation: Strains of K.lactis lacking KIPdc1p (Klpdc1Δ) have been shown to producesignificantly lower levels of ethanol when grown on glucose (Bianchi,M., et al., (1996). “The petite negative yeast Kluyveromyces lactis hasa single gene expressing pyruvate decarboxylase activity”. MolecularMicrobiology 19(1):27-36). To confirm this phenotype, fermentations withstrains GEVO1287 and GEVO1742 were carried out. Briefly, a saturatedovernight (3 mL) culture of each strain grown in YPD was inoculated into25 mL of YPD at a starting OD₆₀₀ of 0.1 and grown aerobically in aloosely-capped flask in a shaker for 24 hours at 30° C., 250 rpm.Following growth, 2 mL of culture were collected, the cells pelleted bycentrifugation (5 minutes, 14,000×g) and the supernatant subjected toanalysis by gas chromatography and liquid chromatography. A summary ofthe data from these analyses is summarized in Table EX1-2. The stronglydiminished production of ethanol and the increased accumulation ofpyruvate in the fermentation medium are characteristic of K.lactisstrains in which PDC1 has been deleted. Thus, these observations confirmthe molecular genetics conclusions that strain GEVO1742 is in factKlpdc1Δ.

TABLE EX1-2 Ethanol and pyruvate produced and glucose consumed inaerobic fermentations of GEVO1287 and GEVO1742. Ethanol Pyruvate GlucoseSTRAIN produced (g/L) produced (g/L) consumed (g/L) GEVO1287 8.129 (notdetected) 17.56 GEVO1742 0.386 1.99 5.25

Example 2 Construction and Confirmation of PDC Deletion in S. cerevisiae

The purpose of this Example is to describe how a PDC deletion variant ofa member of the Saccharomyces sensu stricto yeast group, theSaccharomyces yeast clade, a Crabtree-positive yeast, and a post-WGDyeast, S. cerevisiae was constructed and confirmed.

Strains GEVO1537 and GEVO1538 were incubated in 1% potassium acetate for3-4 days which induces sporulation. The resulting haploid spores wererecovered by random spore analysis. Briefly, a culture of sporulatingcells was examined microscopically to ensure that a sufficient fractionof cells had sporulated (>10%). Five (5) mL of a culture of sporulatedcells were collected by centrifugation (5 minutes at 3000×g) and washedonce in 1 mL of water. The cells were resuspended in 5 mL water to whichwas added 0.5 mL of a 1 mg/mL solution (freshly made) of Zymolyase-T (inwater) as well as 10 μL of β-mercaptoethanol. The cell suspension wasincubated overnight at 30° C. in a shaker at 50 rpm. Five mL of 1.5%Triton X-100 were added and the mixture was incubated on ice for 15minutes. The solution was sonicated three times for 30 seconds per cycleat 50% power, with 2 minutes rest on ice in between sonication cycles.The suspension was centrifuged (1200×g, 5 minutes) and washed twice with5 mL of water. The final cell pellet was resuspended in 1 mL water andcells were plated to YP+2% EtOH.

Following this procedure, the separate individual spores, were platedonto solid medium to obtain colonies, all of genotype HO pdc1::Tn5blepdc5::Tn5ble pdc6:APT1 HIS3 LEU2 TRP1 URA3 and of unknown mating type.Some fraction of the cells were (homozygous) diploid due to the HO+ genestatus and resultant mating type switching and re-mating to formdiploids.

The genotype of the mating type locus of the putative Pdc-minus colonieswas confirmed by PCR using Taq DNA polymerase (New England BioLabs,Ipswich, Mass.) under standard conditions using primers specific for theMAT α locus (primers #489 and #491) or MAT α locus (primers #490 and#491). Colonies that generated a single PCR product with one of the twopossible primer sets primer set and no product when tested with theother were putative haploid Pdc-minus strains. To confirm the matingtype, such strains were crossed to Gevo1187 and Gevo1188 (CEN.PK).Resulting diploid progeny were selected on medium containing glucose (toselect for the presence of PDC+ genes introduced by CEN.PK background)and also lacking at least one of the following nutrients: histidine,leucine, tryptophan, or uracil (to select for the appropriateprototrophy as provided by the wild-type allele of the correspondinggene from the Gevo1537 or GEVO1538 background.

Diploid cells were sporulated and germinated on agar plates containingYP +2% ethanol (to permit growth of Pdc-minus isolates). To identifyPdc-minus candidates, viable colonies were streaked on to YPD agarplates and colonies that were inviable on glucose were isolated.Inability to grow on glucose confirms that these candidates arepdc1::ble and pdc5::ble. The pdc6::apt1 was confirmed their ability togrow on YP+Ethanol plates containing the antibiotic G418.The genotype ofthe mating type locus of the putative Pdc-minus colonies was confirmedby PCR using Taq DNA polymerase (New England BioLabs, Ipswich, Mass.)under standard conditions using primers specific for the MAT α locus(primers #489 and #491) or MAT α locus (primers #490 and #491). Thepresence of a product from both sets of PCR reactions indicated thatboth mating type alleles were present in the population, as aconsequence of mating type allele switching by an active HO-encodedenzyme. The presence of a PCR product for one set of MAT locus-specificprimers but not the other indicated that the strain lacks this activityand was therefore ho−. Based upon these analyses, six candidatescolonies were identified as ho− strains and one candidate #4 was HO.

These Pdc-minus strains were streaked to SC+Ethanol plates lacking oneof: leucine, histidine, tryptophan, or uracil, to determine presence ofauxotrophic mutations within these strains. One Pdc-minus strain,GEVO1581, was auxotrophic for histidine, uracil, and tryptophan, andthus carried three of the makers (his3, ura3, and trp1). AnotherPdc-minus strain, GEVO1715, was auxotrophic for uracil and leucine andthus carried the two markers, ura3 and leu2.

GEVO1581 and GEVO1715 were screened by RFLP analysis to verify thepresence of the ho allele. A 447 by portion of the HO locus wasamplified by PCR that contained the codon that is altered in the hoallele (H475L) using primers 1375 and 1376. This mutation introduces anAluI restriction site, and consequently, digestion with AluI (NewEngland BioLabs, Ipswich, Mass.) yielded either a 447 bp fragment (HO)or a 122 by fragment plus a 325 by fragment (ho). Based upon RFLPanalysis, GEVO1581 was HO and GEVO1715 was ho.

To obtain a Pdc-minus strain with all four auxotrophic markers, GEVO1715was crossed to GEVO1188 and diploids generated as described above. Theresulting diploid was sporulated and Pdc-minus candidates were isolatedby plating onto YP+Ethanol containing both Phleomycin and G418. Thesecandidates were then streaked onto YPD agar plates and tested for theirinviability on glucose. Those that did not grow on glucose were isolatedas this phenotype, in addition to their resistance to Phleomycin andG418 confirms that these candidates are pdc1::ble, pdc5::ble andpdc6::apt1. These isolates were streaked to SC+Ethanol plates lackingone of: leucine, histidine, tryptophan, or uracil, to determine presenceof auxotrophic mutations within these strains. One of these Pdc-minusstrains, GEVO1584, was auxotrophic for histidine, uracil, tryptophan andleucine and thus carried all four markers, his3, ura3, trp1, and leu2.GEVO1584 was also confirmed to be MATa and ho by colony PCR and RFLPanalysis, respectively, as described above.

TABLE EX2-1 Summary table of S. cerevisiae Pdc-minus strains obtainedGEVO No. GENOTYPE STRAIN SOURCE 1537 MAT a/α, HIS3, LEU2, TRP1, URA3,Strain GG570 from Paul van pdc1::ble/pdc1::ble, pdc5::ble/pdc5::ble,Heusden, Univ. of Leiden, pdc6::apt1(kanR)/pdc6::apt1(kanR), HO/HONetherlands 1538 MAT a/α, HIS3, LEU2, TRP1, URA3, Strain GG570 from Paulvan pdc1::ble/pdc1::ble, pdc5::ble/pdc5::ble, Heusden, Univ. of Leiden,pdc6::apt1(kanR)/pdc6::apt1(kanR), HO/HO Netherlands 1581 MAT a/α,his3/his3, trp1/trp1, ura3/ura3, candidate #4 LEU2/LEU2,pdc1::ble/pdc1::ble, GEVO1537 × GEVO1187 pdc5::ble/pdc5::ble,pdc6::apt1(kanR)/pdc6::apt1(kanR), HO/HO 1584 MAT a, his3, trp1, ura3,leu2, pdc1::ble, pdc5::ble, candidate #201 pdc6::apt1(kanR), ho GEVO1715× GEVO1188 1715 MAT a, leu2, ura3, pdc1::ble, pdc5::ble, candidate #104pdc6::apt1(kanR), ho GEVO1187 × GEVO1537

Example 3 Other Pdc-Minus S. cerevisiae Strains.

S. cerevisiae engineered to be deficient in PDC activity have beenpreviously described: (Flikweert, M. T., van der Zanden, L., Janssen, W.M. T. M, Steensma, H. Y., van Dijken J. P., Pronk J. T. (1996) Yeast12(3):247-57). Such strains may be obtained from these sources.

Example 4 Chemostat Evolution of S. cerevisiae PDC Triple-Mutant

This example demonstrates that a PDC deletion variant of a memberSaccharomyces sensu stricto yeast group, the Saccharomyces clade yeast,Crabtree-positive, post-WGD yeast, S. cerevisiae, can be evolved so thatit does not have the requirement for a two-carbon molecule and has agrowth rate similar to the parental strain on glucose.

A DasGip fermentor vessel was sterilized and filled with 200 ml of YNB(Yeast Nitrogen Base; containing per liter of distilled water: 6.7 g YNBwithout amino acids from Difco, the following were added per liter ofmedium: 0.076 g histidine, 0.076 g tryptophan, 0.380 g leucine, and/or0.076 g uracil; medium was adjusted pH to 5 by adding a few drops of HCLor KOH) and contained 2% w/v ethanol. The vessel was installed and allprobes were calibrated according to DasGip instructions. The vessel wasalso attached to an off-gas analyzer of the DasGip system, as well as toa mass spectrometer. Online measurements of oxygen, carbon dioxide,isobutanol, and ethanol were taken throughout the experiment. The twoprobes that were inside the vessel measured pH and dissolved oxygenlevels at all times. A medium inlet and an outlet were also set up onthe vessel. The outlet tube was placed at a height just above the 200 mllevel, and the pump rate was set to maximum. This arrangement helpedmaintain the volume in the vessel at 200 ml. Air was sparged into thefermentor at 12 standard liters per hour (slph) at all times. Thetemperature of the vessel was held constant at 31.8° C. and theagitation rate was kept at 300 rpm. The off-gas was analyzed for CO₂,O₂, ethanol and isobutanol concentrations. The amount of carbon dioxide(X_(CO2)) and oxygen (X_(O2)) levels in the off-gas were used to assessthe metabolic state of the cells. An increase X_(CO2) levels anddecrease in X_(O2) levels indicated an increase in growth rate andglucose consumption rate. The ethanol levels were monitored to ensurethat there was no contamination, either from other yeast cells or frompotential revertants of the mutant strain since the S. cerevisiae PDCtriple-mutant (GEVO1584) does not produce ethanol. The minimum pH in thevessel was set to 5, and a base control was set up to pump in potassiumhydroxide into the vessel when the pH dropped below 5.

GEVO1584 was inoculated into 10 ml of YNB medium with 2% w/v ethanol asthe carbon source. The culture was incubated at 30° C. overnight withshaking. The overnight culture was used to inoculate the DasGip vessel.Initially, the vessel was run in batch mode, to build up a high celldensity. When about 3 g CDW/L of cell biomass was reached, the vesselwas switched to chemostat mode and the dilution of the culture began.The medium pumped into the vessel was YNB with 7.125 g/L glucose and0.375 g/L of acetate (5% carbon equivalent). The initial dilution ratewas set to 0.1 h⁻¹, but as the cell density started dropping, thedilution rate was decreased to 0.025 h⁻¹ to avoid washout. GEVO1584 wasmating type a. A PCR check for the mating type of the chemostatpopulation several days into the experiment indicated that the strainstill present was mating type a.

The culture in the chemostat was stabilized and the dilution rateincreased to 0.1 h⁻¹. After steady state was reached at the 0.1 h⁻¹dilution rate, the concentration of acetate was slowly decreased. Thiswas achieved by using a two pump system, effectively producing agradient pumping scheme. Initially pump A was pumping YNB with 7.125 g/Lglucose, and 0.6 g/L of acetate at a rate of 12.5 mL/h and pump C waspumping YNB with only 7.125 g/L glucose at a rate of 7.5 mL/h. Thecombined acetate going into the vessel was 0.375 g/L. Then, over aperiod of 3 weeks, the rate of pump A was slowly decreased and the rateof pump C was increased by the same amount so that the combined rate offeeding was always 20 mL/h. When the rate of pump A dropped below 3 mL/hthe culture started to slowly wash out. To avoid complete washout thedilution rate was decreased to 0.075 h⁻¹ from 0.1 h⁻¹ (FIG. 5). At thisdilution rate, the rate of pump A was finally reduced to 0, and theevolved strain was able to grow on glucose only. Over the period ofabout five weeks, a sample was occasionally removed, either from thevessel directly or from the effluent line. Samples were analyzed forglucose, acetate, and pyruvate using HPLC, and were plated on YNB withglucose, YNB with ethanol, and YNB (w/o uracil) plus glucose or ethanolas negative control. Strains isolated from the chemostat did not grow onthe YNB plates without uracil. OD₆₀₀ was taken regularly to make surethe chemostat did not wash out. Freezer stocks of samples of the culturewere made regularly for future characterization of the strains.

To characterize growth of the evolved strains YNB, YPD (yeast extract,peptone, dextrose), and YPE (yeast extract, peptone, ethanol) were usedwith various concentrations of glucose or ethanol. The growthcharacterization was performed in either snap-cap test tubes or 48-wellplates (7.5 ml). The snap-cap test tubes were not closed completely sothat air would vent in/out of the tubes, and the 48-well plates werecovered with an air permeable membrane to allow for oxygen transfer. Tocheck for contaminations, YPD or YPE agar plates were used with theantibiotics G418 and Phleomycin. The PDC triple mutant strain (GEVO1584)has both G418 and Phleomycin resistance markers, so the progeny of thatstrain were able to grow on the antibiotics. Single colonies isolatedfrom each chemostat sample were studied for growth rates. A singlecolony isolated from the 35-day chemostat population was selectedbecause of high growth rates on glucose as a sole carbon source, wasresistant to both G418 and Phleomycin, and grew without the need forethanol or acetate. The single colony was further evolved through 24successive serial transfers in test tubes on YPD at 30° C., 250 rpmshaking. The resulting strain, GEVO1863, grew similarly to the wild-typeyeast parent on glucose (FIG. 6), did not produce ethanol (FIG. 7), anddid not require ethanol or acetate for growth.

Example 5 Isobutanol Production in Pdc-plus K. lactis

This example demonstrates isobutanol production in a member of theSaccharomyces clade, Crabtree-negative, pre-WGD yeast, K lactis.

The isobutanol production pathway was cloned in a K. lactis vector-basedexpression system: a SacI-MluI fragment containing the TEF1 promoter.Lactococcus lactis alsS and part of the CYC1 terminator sequence wascloned into the same sites of the K. lactis expression plasmid, pGV1430(FIG. 11), to generate pGV1472 (FIG. 13, SEQ ID NO: 2). A SacI-MluIfragment containing the TEF1 promoter, E. coli ilvD, TDH3 promoter, E.coli ilvC, and part of the CYC1 terminator was cloned into the samesites of the K. lactis expression plasmid, pGV1429 (FIG. 10), togenerate pGV1473 (FIG. 14, SEQ ID NO: 3). A BssHII-NotI fragmentcontaining the TEF1 promoter, L. lactis kivD, TDH3 promoter and S.cerevisiae ADH7. ScAdh7 was cloned into the K. lactis expressionplasmid, pGV1431 (FIG. 12), to obtain pGV1475 (FIG. 15, SEQ ID NO: 4).

The K. lactis strain GEVO1287 was transformed with the above plasmids,pGV1472, pGV1473, and pGV1475 (Table EX5-1) to express the isobutanolpathway. As a control, K. lactis GEVO1287was also transformed with emptyvectors pGV1430, pGV1429, and pGV1431 (Table EX5-1).

TABLE EX5-1 K. lactis clones expressing an isobutanol pathway clone HostPlasmid 1 Plasmid 2 Plasmid 3 ALS KARI DHAD KIVD ADH iB165 GEVO1287pGV1430 pGV1429 pGV1431 — — — — — iB173 GEVO1287 pGV1472 pGV1473 pGV1475Ptef1- Ec. Ec. ilvD Ll. Sc. Ll. ilvC Kivd Adh7 alsS

Transformed cells were grown overnight and transferred to 100 mLfermentation bottles using 20 mL SC-WLU medium. Two mL samples weretaken at 24 and 48 hours for GC analysis. At each time point, 2 mL of a20% glucose was added after removing samples for GC analysis. At 48hours the fermentation was ended. GC samples were processed asdescribed. Results are shown in Table EX5-2 Up to 0.25 g/L isobutanolwas produced in K. lactis transformed with an isobutanol pathway whereasthe control strain without the pathway only produced 0.022 g/L in 48hours.

TABLE EX5-2 K. lactis fermentation results Isobutanol titer Isobutanolyield Ethanol clone (mg/L) (% theoretical) (g/L) iB165 0.022 0.13 11.4iB173 0.25 1.5 12.6

To determine if isobutanol titers can be increased by using a richcomplex media, fermentations were performed as described above withiB165 (vector only control) and iB173 using YPD instead of SC-WLUmedium. In addition, fermentations were also carried out in 250 mLscrew-cap flasks (microaerobic conditions) and in 125 mL metal-capflasks (aerobic conditions). Samples were taken at 24, 48, and 72 andthe isobutanol levels obtained are shown in Table EX5-3.

TABLE EX5-3 K. lactis fermentation results using YPD IsobutanolIsobutanol yield Ethanol clone Condition titer (mg/L) (% theoretical)(g/L) iB165 Anaerobic 66 0.4 27.4 iB165 Microaerobic 117 0.7 24.5 iB165Aerobic 104 0.6 11.7 iB173 Anaerobic 297 1.8 25.8 iB173 Microaerobic 4362.6 23.4 iB173 Aerobic 452 2.7 13.4

Example 6 Isobutanol Production in Pdc Plus S. cerevisiae

This example demonstrates isobutanol production in a member ofSaccharomyces sensu stricto group, Saccharomyces clade,Crabtree-positive, post-WGD yeast, S. cerevisiae.

Various plasmids carrying the isobutanol production pathway wereconstructed for expression of this metabolic pathway in a Pdc-plusvariant of S. cerevisiae, GEVO1187. Plasmids pGV1254 (FIG. 16; SEQ IDNO: 10), pGV1295 (FIG. 17; SEQ ID NO: 11) pGV1390 (FIG. 18; SEQ ID NO:12), and pGV1438 (FIG. 19; SEQ ID NO: 13) were high copy S. cerevisiaeplasmids that together expressed the five genes of the isobutanolpathway (TABLE EX6-1). pGV1390 was generated by cloning a SalI-BamHIfragment containing the L. lactis alsS (SEQ ID NO: 5) into the high copyS. cerevisiae expression plasmid, pGV1387, where the L. lactis alsSwould be expressed under the CUP1 promoter. pGV1295 was generated bycloning a SalI-BamHI fragment containing the E. coli ilvC (SEQ ID NO: 6)into the high copy S. cerevisiae expression plasmid, pGV1266, where theE. coli ilvC would be expressed using the TDH3 promoter. pGV1438 wasgenerated by cloning a SalI-BamHI fragment containing the E. coli ilvD(SEQ ID NO: 7) into the high copy S. cerevisiae expression plasmid,pGV1267, where the E. coli ilvD would be expressed using the TDH3promoter. pGV1254 was made by cloning an EcoRI (filled in by Klenowpolymerase treatment)—XhoI fragment containing the TDH3 promoter and S.cerevisiae ADH2 from pGV1241 into the BamHI (filled in by Klenow) andXhoI sites of pGV1186. pGV1186 was made by cloning a SalI-BamHI fragmentcontaining the L. lactis kivD (SEQ ID NO: 8) into a high copy S.cerevisiae expression plasmid, pGV1102, where the L. lactis kivD wouldbe expressed using the TEF1 promoter. pGV1241 was made by cloning aSalI-BamHI fragment containing the S. cerevisiae ADH2 (SEQ ID NO: 9)into a high copy S. cerevisiae expression plasmid, pGV1106, where the S.cerevisiae ADH2 would be expressed using the TDH3 promoter.

GEVO1187 was transformed with plasmids as shown in Table EX6-1. As adefective isobutanol pathway control, cells were transformed withpGV1056 (FIG. 23, empty vector control) instead of pGV1390. Thetransformants were plated onto appropriate selection plates. Singlecolonies from the transformation were isolated and tested for isobutanolproduction by fermentation.

TABLE EX6-1 Plasmid pGV# Promoter Gene Plasmid type marker pGV1254 ScTEF1 L. lactis kivD High copy Sc URA3 pGV1295 Sc TDH3 E. coli ilvC Highcopy Sc TRP1 pGV1390 Sc CUP1 L. lactis alsS High copy Sc HIS3 pGV1438 ScTDH3 E. coli ilvD High copy Sc LEU1

The cells were grown overnight and anaerobic batch fermentations werecarried out as described in General Methods. SC-HWUL was used as themedia. 2 mL samples were taken at 24, 48 and 72 hours for GC At eachtime point, the cultures were fed 2 mL of a 40% glucose solution. Thefermentation was ended after 72 hours. Samples were processed andanalyzed as described. The results are shown in Table EX6-2. As shown,isobutanol was produced in GEVO1187 transformed with theisobutanol-pathway containing plasmids.

TABLE EX6-2 Isobutanol production in S. cerevisiae, GEVO1187, after 72hours Isobutanol Ethanol Titer Yield Titer Yield Strain Plasmids [g L⁻¹][%] [gL⁻¹] [%] GEVO1187 pGV1254, pGV1438, 0.13 0.31 31 60 pGV1390,pGV1438 GEVO1187 pGV1056, pGV1295, 0.04 0.10 42 82 pGV1438, pGV1254

This example demonstrates isobutanol production in a Pdc-minus member ofthe Saccharomyces clade, Crabtree-negative, pre-WGD yeast, K. lactis.

Description of plasmids pGV1590, pGV1726, pGV1727: pGV1590 (FIG. 20, SEQID NO: 14) is a K. lactis expression plasmid used to express L. lactiskivD (under TEF1 promoter) and S. cerevisiae ADH7 (under TDH3 promoter).This plasmid also carries the K. marxianus URA3 gene and the 1.6 micronreplication origin that allow for DNA replication in K. lactis. pGV1726(FIG. 21, SEQ ID NO: 15) is a yeast integration plasmid carrying theTRP1 marker and expressing B. subtilis aisS using the CUP1 promoter.pGV1727 (FIG. 22, SEQ ID NO: 16) is a yeast integration plasmid carryingthe LEU2 marker and expressing E. coli ilvD under the TEF1 promoter andE. coli ilvC under the TDH3 promoter. Neither pGV1726 or pGV1727 carry ayeast replication origin.

Construction of GEVO1829, a K. lactis strain with pathway integrated:The isobutanol pathway was introduced into the Pdc-minus K. lactisstrain GEVO1742 by random integrations of the pathway genes. GEVO1742was transformed with the Acc65I-NgoMIV fragment of pGV1590 containingthe L. lactis kivd and S. cerevisiae ADH7 but without the yeastreplication origin, to generate GEVO1794. The presence of both L. lactiskivd and S. cerevisiae ADH7 was confirmed by colony PCR using primersets 1334+1335 and 1338+1339, respectively. GEVO1794 was transformedwith pGV1727, a yeast integration plasmid carrying E. coli ilvD (underthe TEF1 promoter) and E. coli ilvC (under TDH3 promoter), that had beenlinearized by digesting with BcgI. The resulting strain, GEVO1818, wasconfirmed by colony PCR for the presence of E. coli ilvD and E. coliilvC using primer sets 1330+1331 and 1325+1328, respectively. GEVO1818was then transformed with pGV1726, a yeast integration plasmid carryingB. subtilis alsS (under the CUP1 promoter), that had been linearized bydigesting with Ahdl to generate GEVO1829. The presence of B. subtilisalsS was confirmed by colony PCR using primers 1321+1324.

Aerobic fermentations were carried out to test isobutanol production bythe Pdc-minus strain carrying the isobutanol pathway, GEVO1829. ThePdc-minus strain without the isobutanol pathway, GEVO1742, was used as acontrol. These strains were cultured in YPD overnight at 30° C., 250rpm, then diluted into 20 mL fresh YPD in a 125 mL flask and grown at30° C., 250 rpm. 2 mL samples were taken at 24 and 48 hours, cellspelleted for 5 minutes at 14,000×g and the supernatant was analyzed forisobutanol by GC. In addition glucose concentrations were analyzed byLC. The results are shown in Table EX7-1. At 48 hours, the OD of theGEVO1742 strain had reached over 8.5 while the OD of the GEVO1829 wasless than 5. GEVO1829 consumed around 15.7 g/L glucose while GEVO1742consumed roughly 7.7 g/L glucose. GEVO1829 produced 0.17 g/L isobutanolwhile GEVO1742 did not produce any isobutanol above media background.

TABLE EX7-1 K. lactis fermentation results Isobutanol titer Isobutanolyield Ethanol Clone (mg/L) (% theoretical) (mg/L) GEVO1742 0 0 17GEVO1829 170 2.6 53

Example 8A Isobutanol Production in Pdc-Minus S. cerevisiae GEVO1581

This example demonstrates isobutanol production in a Pdc-minus member ofthe Saccharomyces sensu stricto group, Saccharomyces clade yeast,Crabtree-positive yeast, post-WGD yeast, S. cerevisiae.

Strain GEVO1581 with the three genes encoding PDC activity deleted(pdc1Δ, pdc5Δ, and pdc6Δ) was used to produce isobutanol. Isobutanolpathway enzymes were encoded by genes cloned into three plasmids.pGV1103 (FIG. 26, SEQ ID NO: 20), pGV1104 (FIG. 27, SEQ ID NO: 21) andpGV1106 (FIG. 28, SEQ ID NO: 22) were empty high copy expression vectorsthat carry as marker genes, URA3, HIS3 and TRP1, respectively. The B.subtilis alsS gene, express using the CUP1 promoter, was encoded oneither a low copy CEN plasmid, pGV1673 (FIG. 32, SEQ ID NO: 26) or ahigh copy plasmid, pGV1649 (FIG. 29, SEQ ID NO: 23). Both of theseplasmids used TRP1 as a marker gene. E. coli ilvD (expressed using theTEF1 promoter) and E. coli ilvC (expressed using the TDH3 promoter) wereexpressed off of the high copy plasmid pGV1677 (FIG. 33, SEQ ID NO: 27).This plasmid utilized HIS3 as a marker gene. L. lactis kivD (expressedusing the TEF1 promoter) and S. cerevisiae ADH7 (expressed using theTDH3 promoter) were expressed off of the high copy plasmid pGV1664 (FIG.30, SEQ ID NO: 24). This plasmid utilized URA3 as a marker gene.Combination of these plasmids (Table EX8-1) to reconstitute theisobutanol pathway were introduced into GEVO1581 by lithium acetatetransformation (described in General Methods).

TABLE EX8-1 Plasmids transformed into GEVO1581 Fermentation # StrainPlasmids Notes iB250 GEVO1581 pGV1103, Vector Control pGV1104, pGV1106iB251 GEVO1581 pGV1677, iBuOH Pathway, alsS on pGV1649, 2 micron plasmidpGV1664 iB252 GEVO1581 pGV1677, iBuOH Pathway, alsS on pGV1673, CENplasmid pGV1664

Fermentation experiments were carried out with GEVO1581 transformed withplasmids according to Table EX8-1 to determine the amount of isobutanolproduced (titer) and the percentage of isobutanol to consumed glucose(yield).

Fermentations with Transformants of GEVO1581: Using cells grown in 3 mLdefined (SC-Ethanol) medium, 20 mL cultures were inoculated withtransformants of GEVO1581 (3 independent colonies per transformationset) to an OD₆₀₀ of approximately 0.1. The cultures were incubated at30° C. at 250 RPM in 125 mL metal cap flasks until they reached an OD₆₀₀of approximately 1. Glucose was added to a final concentration of 5% anda 2 mL aliquot was removed from each sample (T=0 sample). The OD₆₀₀ ofeach sample was measured, the cells in each sample were pelleted bycentrifugation (14,000×g, 5 min), and the supernatant from each samplewas stored at −20° C. The remaining cultures were incubated at 30° C. at125 RPM for another 48 hours. Samples (2 mL) were removed after 24 and48 hours and prepared as just described. The samples were thawed, andprepared as described in General Methods. Three individual transformantswere used for each set of plasmids during the fermentations. The amountof glucose consumed and the amount of pyruvate, glycerol, ethanol, andisobutanol produced after 48 hours are listed in Table EX8A-2.

TABLE EX8A-2 48 hour time point data are shown as an average of threereplicates Glucose consumed (g/L) Isobutanol (mg/L) Yield (%theoretical) iB250 3.6 ± .7  4.7 ± 0.00  0.31 ± 0.04 iB251  2.8 ± 1.6122 ± 41  11.0 ± 5.0 iB252 1.2 ± .5 62 ± 11 12.8 ± 2.8Again using cells grown in 3 mL defined (SC-Ethanol) medium, 20 mLcultures were inoculated with transformants of GEVO1581 to an OD₆₀₀ ofapproximately 0.1. The cultures were incubated at 30° C. at 250 RPM in125 mL metal cap flasks until they reached an OD₆₀₀ of approximately 1.Biomass was pelleted and resuspended in 20 ml media with 2% glucose asthe sole carbon source and a 2 mL aliquot was removed from each sample(T=0 sample). The OD₆₀₀ of each sample was measured and each sample wasstored at −20° C. The remaining cultures were incubated at 30° C. at 125RPM for another 48 hours. Samples (2 mL) were removed after 24 and 48hours and stored at −20° C. The samples were thawed, and prepared asdescribed in General Methods. The amounts of ethanol and isobutanolproduced after 48 hours are listed in Table EX8A-3.

TABLE EX8A-3 48 hour time point data for fermentation in glucose, shownas an average of three replicates Isobutanol Isobutanol yield EthanolEthanol yield (mg/L) (% theoretical) (mg/L) (% theoretical) iB250 0 0 00 iB251 210 3.5 110 1.8

Example 8B Isobutanol Production in Pdc-Minus S. cerevisiae GEVO1584

This example demonstrates isobutanol production in a Pdc-minus member ofthe Saccharomyces sensu stricto group, Saccharomyces clade,Crabtree-positive yeast, WGD yeast, S. cerevisiae.

GEVO1581 is a diploid strain, thus, a second backcross of a Pdc-minusyeast into the CEN.PK background was performed, yielding a Pdc-minushaploid strain GEVO1584 with the required auxotrophic markers forplasmid propagation.

Transformations of GEVO1584: The following combinations of plasmids weretransformed into GEVO1584 (Table EX8B-1) using lithium acetatetransformation (described in General Methods) followed by selection onappropriate minimal media. pGV1672 (FIG. 31, SEQ ID NO: 25), pGV1056(FIG. 23, SEQ ID NO: 17), and pGV1062 (FIG. 24, SEQ ID NO: 18) wereempty low copy CEN expression vectors that carry as marker genes, TRP1,HIS3, and URA3. pGV1103 (FIG. 26, SEQ ID NO: 20), pGV1104 (FIG. 27, SEQID NO: 21) and pGV1102 (FIG. 25, SEQ ID NO: 19) were empty high copyexpression vectors that carry as marker genes, URA3, HIS3 and TRP1,respectively. The isobutanol pathway was expressed off of low copy CENplasmids pGV1673 (FIG. 32, SEQ ID NO: 26), pGV1679 (FIG. 34, SEQ ID NO:28) and pGV1683 (FIG. 35, SEQ ID NO: 29). pGV1673 carried the B.subtilis alsS under the CUP1 promoter and utilized the TRP1 marker gene.pGV1679 carried the E. coli ilvD and E. coli ilvC genes expressed usingthe TEF1 and TDH3 promoters, respectively, and utilized the HIS3 markergene. pGV1683 carried the L. lactis kivd and the S. cerevisiae ADH7genes expressed using the TEF1 and TDH3 promoters, respectively, andutilized the URA3 marker gene. The isobutanol pathway was also expressedoff of high copy plasmids pGV1649 (FIG. 29, SEQ ID NO: 23), pGV1677(FIG. 33, SEQ ID NO: 27) and pGV1664 (FIG. 30, SEQ ID NO: 24). pGV1649carried the B. subtilis alsS under the CUP1 promoter and utilized theTRP1 marker gene. pGV1677 carried the E. coli ilvD and E. coli ilvCgenes expressed using the TEF1 and TDH3 promoters, respectively, andutilized the HIS3 marker gene. pGV1664 carried the L. lactis kivd andthe S. cerevisiae ADH7 genes expressed using the TEF1 and TDH3promoters, respectively, and utilized the URA3 marker gene.

TABLE EX8B-1 Fermentation # Strain Plasmids Notes iB300 GEVO1584pGV1672, Vector Control (CEN pGV1056, plasmids) pGV1062 iB301 GEVO1584pGV1673, Isobutanol pathway pGV1679, (CEN plasmids) pGV1683 iB302GEVO1584 pGV1103, Vector Control (2μ plasmids) pGV1104, pGV1102 iB303GEVO1584 pGV1677, Isobutanol pathway (2μ pGV1649, plasmids) pGV1664

Fermentations with Transformants of GEVO1584: Using cells grown in 3 mLdefined (SC) media containing ethanol (SC+Ethanol-HWU), 200 mL cultureswere inoculated with transformants of GEVO1584 and incubated inSC+Ethanol-HWU at 30° C. at 250 RPM in 500 mL shake flasks for 72 hours.The OD₆₀₀ values measured after 72 hours ranged from 1.4 to 3.5. Thecultures were diluted 1:10 into fresh 250 mL SC+Ethanol-HWU media andincubated at 30° C. at 250 RPM in 500 mL shake for 24 hours. The cellswere collected by centrifugation at 3000 RPM for 3 minutes andresuspended in 20 mL SC+Glucose-HWU media in 125 mL metal cap flasks.250 μL of 100% ethanol was added to each culture to bring theconcentration of ethanol to 1%. A 2 mL aliquot was removed, the OD₆₀₀was measured using 100 μL, and the remaining aliquot was centrifuged topellet cells (14,000×g, 5 min) and the supernatants were stored at −20°C. The cultures were incubated at 125 rpm at 30° C. A 2 mL aliquot wasremoved from each culture after 24 and 48 hours of incubation, and theOD₆₀₀ was measured as before (see Table 3, t=24 and t=48) and the samplecentrifuged and stored as described above. The samples were thawed, andthe samples were prepared and analyzed via GC and HPLC as described inGeneral Methods. Results are shown in Table EX8B-2.

TABLE EX8B-2 48 hour time point data are shown as an average of threereplicates Glucose Ethanol Isobutanol Consumed Consumed Fermentation #Titer (g/L) (g/L) (g/L) Yield (% theor.)] iB300 Vector Control 0.012 ±0.003 9.75 ± 4.17 2.47 ± 0.30 0.30% (CEN plasmids) iB301 Isobutanol0.392 ± 0.087 9.31 ± 5.03 0.95 ± 0.64 10.27% pathway (CEN plasmids)iB302 Vector Control 0.013 ± 0.006 8.61 ± 4.51 0.64 ± 0.17 0.37% (2μplasmids) iB303 Isobutanol 0.248 ± 0.032 9.51 ± 1.25 0.77 ± 0.59 6.36%pathway (2μ plasmids)

All Pdc-minus yeast (GEVO1584) consumed approximately 10 g/L of glucoseand less than 2 g/L of ethanol after 48 hours. All strains accumulated˜1.5 g/L pyruvate, except for those carrying the isobutanol pathway on2μ plasmids (<0.5 g/L). The accumulation of pyruvate and failure of theyeast to produce ethanol from glucose is confirmation that all lackedPDC activity. After 48 hours, the Pdc-minus yeast with the isobutanolpathway encoded on 2μ plasmids generated 0.248±0.032 g/L isobutanol at atheoretical yield of 6.36% of the consumed glucose (Table EX8B-2). TheCEN plasmid isobutanol pathway strain generated 0.392±0.087 g/Lisobutanol at a yield of 10.27% (Table EX8B-2). Isobutanol titers werewell above the equivalent vector control strains.

Example 9 High-Yield Isobutanol Fermentation Using Crabtree-NegativePDC-Minus and GPD-Minus K. lactis

In yeast, excess NADH is oxidized to NAD+ through the generation ofglycerol. The key enzyme involved in this reaction is the glycerol3-phosphate dehydrogenase. Deletion of the gene encoding this protein,KI-Gpd1p, would eliminate loss of NADH as well as carbons from glucose.This would lead to an increased yield of isobutanol.

The PDC-minus K. lactis strain, GEVO1488, is engineered to delete GPD1gene of K. lactis. This PDC-minus GPD-minus strain is transformed withpGV1565 and pGV1568 (FIG. 36 and FIG. 37). These transformants are thensubjected to anaerobic batch fermentation and samples analyzed asdescribed. As shown in Table EX9-1, the additional deletion of GPD1 isexpected to result in a significant increase in isobutanol yield.

Example 10 High-Yield Isobutanol Fermentation Using Crabtree-NegativePDC-Minus and GPD-Minus K. lactis with Balanced Isobutanol Pathway

Yield is further increased by the use of a pathway in which there is abalanced usage of NADH and NADPH. This balance is accomplished by theuse of an engineered ilvC which is able to utilize NADH and theNADH-dependent alcohol dehydrogenase, Adh2. These constructs are used toexpress the isobutanol pathway in a PDC-minus and GPD-minus K. lactis.This strain is subjected to anaerobic batch fermentation as describedabove and samples are analyzed for isobutanol. As shown in Table EX9-1,the yield of isobutanol using this pathway in a PDC-minus K. lactis isexpected to result in a significant increase in yield.

Example 11 High-Yield Isobutanol Fermentation Using Crabtree-NegativePDC-Minus and GPD-Minus K. lactis with Balanced Isobutanol Pathway

An alternative route to balancing the NADH and NADPH usage is tooverexpress an NADP⁺-dependent glyceraldehyde 3-phosphate dehydrogenase(GAPDH) in addition to the endogenous NAD⁺-dependent GAPDH, such thatboth NADH and NADPH are generated from glycolysis. The isobutanolpathway can utilize an NADPH-dependent KARI enzyme and theNADH-dependent Adh2p. In this case, PDC-minus and GPD-minus K. lactis istransformed with a construct expressing a NADP+-dependent GAPDH and anisobutanol pathway using Adh2. This strain is subjected to anaerobicbatch fermentation as described above and samples analyzed forisobutanol. As shown in Table EX9-1, introduction of thisNADP⁺-dependent GAPDH is expected to result in a significant increase inproductivity of isobutanol.

Example 12 High-Yield Isobutanol Fermentation Using Crabtree-NegativePDC-Minus and GPD-Minus K. lactis with Balanced Isobutanol Pathway

Yet another alternative route to balancing the NADH and NADPH usage isto replace the endogenous NAD⁺-dependent GAPDH with an NADP⁺-dependentGAPDH in a PDC-minus and GPD-minus K. lactis. This strain is transformedwith the isobutanol pathway and subjected to anaerobic batchfermentation as described above and samples analyzed for isobutanol. Asshown in Table EX9-1, introduction of this NADP⁺-dependent GAPDH isexpected to result in a significant increase in productivity ofisobutanol.

TABLE EX9-1 Isobutanol productivity in K. lactis strains after 48 hours.(Listed numbers for the pdc-minus strains are expected numbers).Isobutanol Ethanol Titer Yield Titer Yield Genotype Plasmid [g L⁻¹] [%][g L⁻¹] [%] PDC+ pathway genes 0.25 1.5 12.6 62 GPD+ pdc− pathway genes8.2 50 0.01 0.05 GPD+ pdc− pathway genes 11.5 70 0.01 0.05 gpd− pdc−balanced pathway 13.2 80 0.01 0.05 gpd− (NADH utilizing pathway) pdc−balanced pathway 13.2 80 0.01 0.05 gpd− (NADH and NADPH production fromglycolysis) pdc− balanced pathway 13.2 80 0.01 0.05 gpd− (NADPHproduction from glycolysis)

Example 13 High-Yield Isobutanol Fermentation Using Crabtree-PositivePDC-Minus and GPD-Minus S. cerevisiae

The PDC-minus S. cerevisiae strain is engineered to delete both GPD1 andGPD2. This PDC-minus GPD-minus strain is transformed with plasmidsexpressing the isobutanol pathway in S. cerevisiae. These transformantsare then subjected to anaerobic batch fermentation and samples analyzedas described. As is seen in Table EX13-1, the additional deletions ofGPD1 and GPD2 is expected to result in a significant increase inisobutanol yield.

Example 14 High-Yield Isobutanol Fermentation Using Crabtree-PositivePDC-Minus and GPD-Minus S. cerevisiae with Balanced Isobutanol Pathway

Yield is further increased by the use of a pathway in which there isbalanced usage of NADH and NADPH usage. This balance is accomplished bythe use of an engineered KARI which is able to utilize NADH and theNADH-dependent alcohol dehydrogenase, Adh2p. These constructs are usedto express the isobutanol pathway in a PDC-minus and GPD-minus S.cerevisiae. This strain is subjected to anaerobic batch fermentation asdescribed above and samples are analyzed for isobutanol. As shown inTable EX13-1, the yield of isobutanol using this pathway in a PDC-minusS. cerevisiae is expected to result in a significant increase in yield.

Example 15 High-Yield Isobutanol Fermentation Using Crabtree-PositivePDC-Minus GPD-Minus S. cerevisiae with Balanced Isobutanol Pathway

An alternative route to balancing the NADH and NADPH usage is tooverexpress an NADP⁺-dependent glyceraldehydes 3-phosphate dehydrogenase(GAPDH) in addition to the endogenous NAD⁺-dependent GAPDH, such thatboth NADH and NADPH are generated from glycolysis. The isobutanolpathway can utilize an NADPH-dependent KARI enzyme and theNADH-dependent Adh2. In this case, PDC-minus and GPD-minus S. cerevisiaeis transformed with a construct expressing a NADP⁺-dependent GAPDH andan isobutanol pathway using Adh2. This strain is subjected to anaerobicbatch fermentation as described above and samples analyzed forisobutanol. As shown in Table EX13-1, introduction of thisNADP⁺-dependent GAPDH is expected to result in a significant increase inproductivity of isobutanol.

Example 16 High-Yield Isobutanol Fermentation Using Crabtree-PositivePDC-Minus S. cerevisiae with Balanced Isobutanol Pathway

Yet another alternative route to balancing the NADH and NADPH usage isto replace the endogenous NAD⁺-dependent GAPDH with an NADP⁺-dependentGAPDH in a PDC-minus and GPD-minus S. cerevisiae. This strain istransformed with the isobutanol pathway and subjected to anaerobic batchfermentation as described above and samples analyzed for isobutanol. Asshown in Table EX13-1, introduction of this NADP⁺-dependent GAPDH isexpected to result in a significant increase in productivity ofisobutanol.

TABLE EX13-1 Isobutanol productivity in S. cerevisiae strains after 48hours. (Listed numbers for the pdc-minus strains are expected numbers).Isobutanol Ethanol Titer Yield Titer Yield Genotype Plasmid [g L⁻¹] [%][g L⁻¹] [%] WT pathway genes 0.13 0.31 31 60 pdc− pathway genes 8.2 500.01 0.05 pdc− pathway genes 9.9 70 0.01 0.05 gpd− pdc− balanced pathway13.2 80 0.01 0.05 gpd− (NADH utilizing pathway) pdc− balanced pathway13.2 80 0.01 0.05 gpd− (NADH and NADPH production from glycolysis) pdc−balanced pathway 13.2 80 0.01 0.05 gpd− (NADPH production fromglycolysis)

Example 17 High-Yield Isobutanol Fermentation Using Crabtree-NegativePDC-Minus GPD-Minus Evolved K. lactis with Balanced Isobutanol Pathway

In an embodiment, the yield for isobutanol may be increased by furtherengineering yeast microorganism to reduce production of minorbyproducts. Isobutanol may be produced at a yield of about 90%theoretical.

Example 18 High-Yield Isobutanol Fermentation Using Crabtree-PositivePDC-Minus GPD-Minus Evolved S. cerevisiae with Balanced IsobutanolPathway

In another embodiment, the yield for isobutanol may be increased byfurther engineering a yeast microorganism to reduce production of minorbyproducts. Isobutanol may be produced at a yield of about 90%theoretical.

General Methods for Examples 19-24

Sample preparation: Samples were prepared from various timepoints foranalysis by liquid chromatography and gas chromatography. 2 mL of mediawas removed and centrifuged at 14,000×g for 10 min. The supernatant wasremoved and stored at 4° C. until analysis.

Determination of optical density: The optical density of the yeastcultures was determined at 600 nm using a DU 800 spectrophotometer(Beckman-Coulter, Fullerton, Calif., USA). Samples were diluted asnecessary to yield an optical density of between 0.1 and 0.8.

Gas Chromatography: Analysis of ethanol and isobutanol was performed ona HP 5890 gas chromatograph fitted with a ZB-FFAP column (Phenomenex; 30m length, 0.32 mm ID, 0.25 μM film thickness) or equivalent connected toa flame ionization detector (FID). The temperature program was asfollows: 200° C. for the injector with Agilent cyclo-splitter insert,300° C. for the detector, 100° C. oven for 1 minute, 70° C./minutegradient to 235° C., and then hold until a final run time of 5.54 min.Injection volume was 0.5 μl, with a split ratio of 50:1; Helium flowrate was approximately 2.3 ml/min using a constant pressure of 0.88 bar.

High Performance Liquid Chromatography: Analysis of glucose and organicacids was performed on a HP-1100 High Performance Liquid Chromatographysystem equipped with two Rezex RFQ-“Fast Fruit” columns in series(Phenomenex, 100×7.8 mm, 8 μm particles), or equivalent, and an H⁺cation guard column (Bio-Rad) or equivalent. Pyruvate and HMF weredetected using an HP-1100 UV detector (210 nm, 8 nm 360 nm reference)while all other organic acids and glucose were detected using an HP-1100refractive index detector. The column and RI temperatures were 60° C.This method was Isocratic with 0.018N sulfuric acid in water as mobilephase. Flow was set at 1.1 mL/min. Injection size was 20 μL and the runtime was 15 minutes

Lithium Acetate transformations of S. cerevisiae strains weretransformed by the Lithium Acetate method (Gietz et al., Nucleic AcidsRes. 27:69-74 (1992). Cells were collected from overnight cultures grownin 50 mL of defined (SC) ethanol media at an OD₆₀₀ of approximately 0.8to 1.0 by centrifugation at 2700 rcf for 2 minutes at room temperature.The cell pellet was resuspended in 50 mL sterile water, collected bycentrifugation (2700 rcf; 2 min; room temp.), and resuspended in 25 mLsterile water. The cells were collected by centrifugation (2700 rcf; 2min; room temp.) and resuspended in 1 mL 100 mM lithium acetate. Thecell suspension was transferred to a sterile 1.5 mL tube and collectedby centrifugation at full speed for 10 seconds. The cells wereresuspended in 100 mM lithium acetate with a volume four times thevolume of the cell pellet (e.g. 400 μM for 100 μM cell pellet). To theprepared DNA Mix (72 μl 50% PEG, 10 μl 1M Lithium Acetate, 3 μl boiledsalmon sperm DNA, and 5 μl of each plasmid), 15 μl of the cellsuspension was added and mixed by vortexing with five short pulses. Thecell/DNA suspensions were incubated at 30° C. for 30 minutes and at 42°C. for 22 minutes. The cells were collected by centrifugation for 10seconds at full speed and resuspended in 100 μl SOS (1M Sorbitol, 0.34%(w/v) Yeast Extract, 0.68% (w/v) Peptone, 6.5 mM CaCl). The cellsuspensions were top spread over appropriate selective agar plates.

Yeast colony PCR: Yeast cells were taken from agar medium andtransferred to 30 μl 0.2% SDS and heated for 4 mins at 90° C. The cellswere spun down and 1 μl of the supernatant was used for PCR usingstandard Taq (NEB).

Molecular biology: Standard molecular biology methods for cloning andplasmid construction were generally used, unless otherwise noted(Sambrook & Russell).

Media:

YP: contains 1% (w/v) yeast extract, 2% (w/v) peptone.

YPD is YP containing 2% (w/v) glucose, YPE is YP containing 2% (w/v)Ethanol.

YPD80 medium (Difco) is YP containing 80 g/L glucose, 0.2 g/L G418antibiotic, 20 μM CuSO₄, and 1% ethanol.

SC+Complete: 20 g/L glucose, 14 g/L Sigma™ Synthetic Dropout Mediasupplement (includes amino acids and nutrients excluding histidine,tryptophan, uracil, and leucine), and 6.7 g/L Difco™ Yeast NitrogenBase. 0.076 g/L histidine, 0.076 g/L tryptophan, 0.380 g/L leucine, and0.076 g/L uracil.

Solid versions of the above described media contain 2% (w/v) agar.

Strains, Plasmids and Primer Sequences for Examples 19-24

TABLE EX 19-1 Genotype of strains for Examples 19-24. GEVO No. Genotypeand/or Reference GEVO2712 S. cerevisiae CEN.PK2; MATa ura3 leu2 his3trp1 pdc1::{P_(CUP1)-Bs_alsS2, TRP1} pdc5::{P_(TEF1):Sc_ILV3ΔNP_(TDH3):Ec_ilvC_coSc^(Q110V), LEU2} pdc6::{P_(TEF1): Ll_kivd2_coEcP_(TDH3):Dm_ADH, URA3}, evolved for C2 supplement-independence, glucosetolerance and faster growth GEVO2843 S. cerevisiae, MATa ura3 leu2 his3trp1 pdc1Δ::P_(CUP1):[Bs_alsS1_coSc:T_(CYC1): P_(PGK1): Ll_kivD2:P_(ENO2): Sp_HIS5] pdc5Δ::[LEU2-bla-P_(TEF1): ILV3ΔN: P_(TDH3):Ec_ilvC_coSc^(Q110V)] pdc6Δ::[URA3: bla; P_(TEF1): Ll_kivD2: P_(TDH3):Dm_ADH] {evolved for C2 supplement-independence, glucose tolerance andfaster growth} GEVO2962 S. cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1pdc1::PCUP1-Bs_alsS_coSc- TCYC1-PPGK1-Ll_kivd-PENO2-Sp_HIS5pdc5::LEU2-bla-PTEF1-ILV3ΔN-PTDH3- ilvC_coSc_Q110Vpdc6::URA3-bla-PTEF1-Ll_kivd-PTDH3-DmADH {evolved for C2supplement-independence, glucose tolerance and faster growth} pGV2227GEVO2994 S. cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)- Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1 {evolved for C2supplement-independence, glucose tolerance and faster growth} GEVO3059S. cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1 gpd1::T_(Kl) _(—)_(URA3) _(—) _(short)-P_(FBA1)- Kl_URA3-T_(Kl) _(—) _(URA3)pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5 pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)-Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1{evolved for C2 supplement-independence, glucose tolerance and fastergrowth} GEVO3061 S. cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1gpd2::T_(Kl) _(—) _(URA3) _(—) _(short)-P_(FBA1)- Kl_URA3-T_(Kl) _(—)_(URA3)pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5 pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)-Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1{evolved for C2 supplement-independence, glucose tolerance and fastergrowth} GEVO3124 S. cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1gpd1::T_(Kl) _(—) _(URA3) _(—) _(short)-P_(FBA1)- Kl_URA3-T_(Kl.URA3)gpd2::P_(CCW12)-Hph pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)- Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1 {evolved for C2supplement-independence, glucose tolerance and faster growth} GEVO3128S. cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1 gpd1::P_(CCW12)-Hphgpd2::T_(Kl) _(—) _(URA3) _(—) _(short)-P_(FBA1)-Kl_URA3-T_(Kl)_URA3pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)- Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1 {evolved for C2supplement-independence, glucose tolerance and faster growth} GEVO3158S. cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1 gpd1::T_(Kl) _(—)_(URA3) _(—) _(short)-P_(FBA1)- Kl_URA3-T_(Kl) _(—) _(URA3)gpd2::P_(CCW12)-Hph pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)- Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1 [pGV2227] {evolved for C2 supplement-independence, glucose tolerance and faster growth} GEVO3159 S.cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1 gpd1::T_(Kl) _(—) _(URA3)_(—) _(short)-P_(FBA1)- Kl_URA3-T_(Kl) _(—) _(URA3) gpd2::P_(CCW12)-Hphpdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)- Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1 [pGV2082] {evolved for C2 supplement-independence, glucose tolerance and faster growth} GEVO3160 S.cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1 gpd1::P_(CCW12)-Hphgpd2::T_(Kl) _(—) _(URA3) _(—) _(short)-P_(FBA1)-Kl_URA3-T_(Kl) _(—)_(URA3) pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_his5pdc5::LEU2-bla-P_(TEF1)-ILV3ΔN20-P_(TDH3)- Ec_ilvC_coSc_Q110Vpdc6::P_(TEF)-Ll_ilvD_coSc_P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1 [pGV2247] {evolved for C2 supplement-independence, glucose tolerance and faster growth} GEVO3532 S.cerevisiae CEN.PK2; MATa ura3 leu2 his3 trp1 gpd1::T_(Kl) _(—) _(URA3)gpd2::T_(Kl) _(—) _(URA3)pdc1::P_(CUP1)-Bs_alsS1_coSc-T_(CYC1)-P_(PGK1)-Ll_kivd2_coEc-P_(ENO2)-Sp_HIS5pdc5::T_(Kl) _(—) _(URA3) _(—) _(short)-P_(FBA1)-Kl_URA3-T_(Kl) _(—)_(URA3) pdc6::P_(TEF1)-Ll_ilvD_P_(TDH3)-Ec_ilvC_coSc^(P2D1-A1)-P_(ENO2)-Ll_adhA-P_(FBA1)-Sc_TRP1 {evolved for C2supplement- independence, glucose tolerance and faster growth} (firstdescribed here)

TABLE EX 19-2 Plasmids disclosed for Examples 19-24. GEVO No. Genotypeor Reference pGV2082 P_(TEF1)-Ll_ilvD_coSc-P_(TDH3)-Ec_ilvC_coSc_Q110V-P_(TPI1)-G418R-P_(PGK1)-Ll_kivD2_coEc-P_(ENO2)-Dm_ADH, 2μ ori, bla, pUC-ori. pGV2227P_(TEF1)-Ll_ilvD_coSc-P_(TDH3)-Ec_ilvC_coSc^(Q110V)-P_(TPI1)-G418R-P_(PGK1)-Ll_kivd2_coEc- PDC1-3′region-P_(ENO2)-Ll_adhA 2μbla, pUC-ori pGV2247P_(TEF1)-Ll_ilvD_coSc-P_(TDH3)-Ec_ilvC_coSc_P2D1-A1-P_(TPI1)-G418R-P_(PGK1)-Ll_kivD2_coEc-P_(ENO2)- Ll_adhA, 2μ ori, bla,pUC-ori. pGV2563 P_(TEF1)-Ll_ilvD_coSc,P_(TDH3)-Ec_ilvC_coSc^(P2D1-A1-his6), P_(ENO2)-Ll_adhA_coSc^(RE1-his6),2μ- ori, pUC ori, bla, G418r

Example 19 Isobutanol Production in Pdc-Yeast

This example demonstrates isobutanol production at greater than 30%yield in a Pdc-minus member of the Saccharomyces sensu stricto group,Saccharomyces clade yeast, Crabtree-positive yeast, post-WGD yeast S.cerevisiae.

GEVO2962 is a modified yeast biocatalyst that contains genes within thechromosome of the biocatalyst which encode a pathway of enzymes thatconvert pyruvate into isobutanol. GEVO2962 is GEVO2843 transformed withpGV2227 (SEQ ID NO: 57), which is a high copy yeast expression plasmidused to overexpress Ec_ilvC_Q110V (Escherichia coli ilvC containing a Qto V mutation at position 110), LI_ilvD (Lactococcus lactis ilvD),LI_kivD2 (Lactococcus lactis kivD), and LI_AdhA (Lactococcus lactisadhA). The strain GEVO2843 is PDC-deficient and able to grow in highglucose media without addition of C2-compounds. GEVO2843 has integratedinto the PDC1 locus the Bs_alsS1_coSc (Bacillus subtilis alsS; SEQ IDNO: 58) and LI_kivD2_coEc (Lactococcus lactis kivD, SEQ ID NO: 59) genesunder the CUP1 and PGK1 promoters, respectively. This strain also hasthe LI_kivD2_coEc (Lactococcus lactis kivD, SEQ ID NO: 59) and Dm_ADH(Drosophila melanogaster ADH, SEQ ID NO: 60) under the TEF1 and TDH3promoters, respectively, integrated into the PDC6 locus. Lastly, thisstrain has the Ec_ilvC_coSc_Q110V (SEQ ID NO: 61) and Sc_ILV3ΔN20 (SEQID NO: 62) under the TDH3 and TEF1 promoters, respectively, integratedat the PDC5 locus.

When the biocatalyst GEVO2962 was contacted with glucose in a mediumsuitable for growth of the biocatalyst, at about 30° C., the biocatalystproduced isobutanol from the glucose. A 24-hour starter culture wasstarted in a 50 mL conical tube with GEVO2962 cells from a frozenglycerol stock. The tube contained a 5 mL volume of YPD80 medium (Difco)at a starting OD₆₀₀ of about 1.0. The starter culture was grown forapproximately 24 hrs in a 30° C. shaker at 250 rpm. The entire contentsof the starter culture were then transferred to a flask seed culture.The flask seed culture was 1 L of YPD80 medium in a 2.8 L baffledFernbach flask. The seed flask culture was grown for approximately 24hrs in a 30° C. shaker at 250 rpm.

A portion of the flask seed culture was transferred to a 2 L DasGip seedfermenter containing about 750 mL of YPD80 medium to achieve a 1 OD₆₀₀initial cell concentration. The fermenter vessel was attached to acomputer control system to monitor and control pH at 5.0 throughaddition of base, temperature at 30° C., oxygen transfer rate (OTR), andagitation. The vessel was agitated, with a fixed agitation of 1000 rpmand 2 sL/h air flow overlay. Cells were grown until the OD₆₀₀ was about10. Some of the seed fermenter culture was then transferred to a 2 LDasGip fermenter vessel containing about 1100 mL of YPD80. The vesselwas attached to a computer control system to monitor and control pH at6.0 through addition of base, temperature at about 30° C., dissolvedoxygen, and agitation. Initially, during the cell growth phase, thevessel was agitated with a variable agitation of 400-600 rpm using a 10sL/h air sparge until the OD₆₀₀ was about 8. Cell growth continued forapproximately 16 hrs, after which time, the agitation was fixed at 600rpm with 5 sL/h airflow. The dissolved oxygen was approximately zerothroughout this experiment with an OTR of about 4-8 mM/h. Continuousmeasurement of the fermentor vessel off-gas by mass spectrometeranalysis was performed for oxygen, isobutanol, ethanol, and carbondioxide throughout the experiment. Samples were aseptically removed fromthe fermenter vessel throughout the experiment and used to measureOD₆₀₀, glucose concentration, and isobutanol concentration in the broth.

At about 48 h intervals throughout the 470 h experiment, the fermenterwhole broth was removed from the fermenter, cells were separated fromthe broth using centrifugation at about 20° C. and 4000×g in 500 mLcentrifuge bottles. The cell pellets were resuspended in fresh YPDmedium that contained 80 g/L glucose, 0.2 g/L G418 antibiotic, 20 μMCuSO₄, and 1% ethanol and returned to the fermenter. At six pointsthroughout the fermentation, about 1 L of a flask culture of GEVO2962 atabout 7 OD₆₀₀ was concentrated to 50-100 mL by centrifugation and thenadded to the fermenter vessel aseptically.

The fermenter vessel was attached by tubing to a smaller 400 mLfermenter vessel that served as a flash tank and operated in arecirculation loop with the fermenter. Whole fermentation broth wasrecirculated between the flash tank and fermenter at a rate of about10-30 mL per min. The volume in the flash tank was approximately 100 mLand the hydraulic retention time in the flash tank was about 3-10minutes. Heat and vacuum were applied to the flash tank. The vacuumlevel applied to the flash tank was initially set at about 60 mBar andthe flash tank was set at approximately 36° C. Generally, the vacuumranged from 50-65 mBar and the flash tank temperature ranged from 35° C.to 37° C. throughout the experiment. Vapor from the heated flash tankwas condensed into a collection vessel as distillate. Whole fermentationbroth was continuously returned from the flash tank back to thefermentation vessel. When the concentration of isobutanol in the brothdropped below 1.5 g/L, the flash recycle system was turned off. Theflash recycle was turned back on when the broth concentration ofisobutanol reached above 2.5 g/L.

The distillate recovered in the experiment was strongly enriched forisobutanol. Isobutanol formed an azeotrope with water and lead to a twophase distillate: an isobutanol rich top phase and an isobutanol leanbottom phase. Distillate samples were analyzed by GC for isobutanolconcentration.

Isobutanol production reached a maximum at around 470 hrs with a totaleffective titer of about 111 g/L. The isobutanol production rate wasabout 0.24 g/L/h on average over the course of the experiment. Thepercent theoretical yield of isobutanol was approximately 36% at the endof the experiment.

Example 20 Isobutanol Production in Pdc-Gpd-Yeast

This example demonstrates isobutanol production at greater than 70%yield in a Pdc-minus, Gpd-minus member of the Saccharomyces sensustricto group, Saccharomyces clade yeast, Crabtree-positive yeast,post-WGD yeast, S. cerevisiae.

The modified yeast biocatalyst, GEVO3158, encodes a heterologous pathwayof enzymes that convert pyruvate into isobutanol. Genes for the pathwayare located on the chromosome and on a single plasmid. GEVO3158 isGEVO3124 transformed with pGV2247 (SEQ ID NO: 63), which is a high copyyeast expression plasmid used to overexpress Ec_ilvC_Q110V (Escherichiacoli ilvC containing a Q to V mutation at position 110), LI_ilvD(Lactococcus lactis ilvD), LI_kivD (Lactococcus lactis kivD), andLI_adhA (Lactococcus lactis adhA). The strain GEVO3124 is bothGPD-deficient, PDC-deficient and able to grow in high glucose mediawithout addition of C2-compounds. GEVO3124 has integrated into the PDC1locus the Bs_alsS1_coSc (Bacillus subtilis alsS; SEQ ID NO: 58) andLI_kivD2_coEc (Lactococcus lactis kivD, SEQ ID NO: 59) genes under theCUP1 and PGK1 promoters, respectively. This strain also has theEc_ilvC_coSc P2D1-A1 (Escherichia coli ilvC variant; SEQ ID NO: 64),LI_ilvD_coSc, and LI_adhA (Lactococcus lactis adhA, SEQ ID NO: 66) underthe TDH3, TEF1 and ENO2 promoters, respectively, integrated into thePDC6 locus. Lastly, this strain has the Ec_ilvC_coSc_Q110V (Escherichiacoli ilvC containing a Q to V mutation at position 110; SEQ ID NO: 61)and Sc_ILV3ΔN20 (SEQ ID NO: 62) under the TDH3 and TEF1 promoters,respectively, integrated at the PDC5 locus.

GEVO3124 was generated by deletion of GPD2 using Hph as marker in strainGEVO3059. Deletion of GPD2 was carried out by transforming a hygromycinresistance marker, Hph, flanked by the GPD2 5′ and 3′ targetingsequences. This gpd2::Hph disruption cassette was generated by multiplerounds of SOE PCR. First, the GPD2 5′ targeting sequence was amplifiedfrom pGV2164 (SEQ ID NO: 69), the CCW12 promoter was amplified frompGV1954 (SEQ ID NO: 70), the Hph ORF was amplified from pGV2074 (SEQ IDNO: 71), and the GPD2 3′ targeting sequence was also amplified. Second,the GPD2 5′ targeting sequence and the CCW12 promoter were stitchedtogether by SOE-PCR, and the Hph ORF and GPD2 3′ targeting sequence werestitched together by SOE-PCR. Lastly, these two SOE-PCR products werestitched together in another round of SOE-PCR. The resulting product wasthen transformed into GEVO3059 recovered overnight in YPD+1% EtOH+G418or YPD+1% EtOH+G418+1 g/L glycerol, and selected on YPD+G418+Hygro+1 g/Lglycerol or YPD+G418+Hygro+10 g/L glycerol plates. Twelve colonies werere-streaked for singles and colony PCRs were performed in single colonyisolates to test for correct 5′ and 3′ junctions and the loss of GPD2.

GEVO3059 was generated by deletion of GPD1 using KI_URA3 as marker instrain GEVO2994. Deletion of GPD1 was carried out by a bipartiteintegration scheme using the KI_URA3 marker. The 5′ bipartite fragmentcontained the GPD1_(—)5′ targeting sequence-T_(KI) _(—) _(URA3) _(—)_(short)-P_(FBA1)-KI_URA3_(—)3′ truncated and was generated by PCR withpGV2359 (SEQ ID NO: 72) as template. The 3′ bipartite fragment containedKI_URA3_(—)5′ truncated-T_(KI) _(—) _(URA3)-GPD1_(—)3′ targetingsequence and was generated by PCR with pGV2157 (SEQ ID NO: 73) astemplate. The 3′ truncated and 5′ truncated KI_URA3 overlapped by 347 byto allow for recombination between the KI_URA3 sequences andreconstitution of a functional KI_URA3 gene. The 5′ and 3′ bipartitefragments were co-transformed into GEVO2994 and selected on SCD-U+1 g/Lglycerol plates.

GEVO2994 was generated by integrating the Ec_ilvC_coSc_P2D1-A1(Escherichia coli ilvC variant; SEQ ID NO: 64), LI_ilvD_coSc,(Lactococcus lactis ilvD, SEQ ID NO: 65) and LI_adhA (Lactococcus lactisadhA, SEQ ID NO: 66) under the TDH3, TEF1 and ENO2 promoters,respectively, into the PDC6 locus of GEVO2843. This integration replacedthe LI_kivD2_coEc (Lactococcus lactis kivD, SEQ ID NO: 59) and theDm_ADH (Drosophila melanogaster ADH, SEQ ID NO: 60) that were present atthe PDC6 locus in GEVO2843. GEVO2843 was generated by integrating theBs_alsS1_coSc (Bacillus subtilis alsS; SEQ ID NO: 58) and LI_kivD2_coEc(Lactococcus lactis kivD, SEQ ID NO: 59) into the PDC1 locus of GEVO2712

When the biocatalyst GEVO3158 was contacted with glucose in a mediumsuitable for growth of the biocatalyst, at about 30° C., the biocatalystproduced isobutanol from the glucose. A 24-hour starter culture wasstarted in a 50 mL conical tube with GEVO3158 cells from a frozenglycerol stock. The tube contained a 5 mL volume of YPD80 at a startingOD₆₀₀ of about 1.0. The starter culture was grown for approximately 24hrs in a 30° C. shaker at 250 rpm. The entire contents of the starterculture were then transferred to a flask seed culture. The flask seedculture was 80 mL of YPD80 medium in a 500 mL baffled Erlenmeyer flask.The seed flask culture was grown for approximately 24 hrs in a 30° C.shaker at 250 rpm.

A portion of the flask seed culture was transferred to a 2 L DasGipfermenter containing about 750 mL of YPD80 medium to achieve a 0.5 OD₆₀₀initial cell concentration. The fermenter vessel was attached to acomputer control system to monitor and control pH at 6.0 throughaddition of base, temperature at 30° C., oxygen transfer rate (OTR), andagitation. The vessel was agitated, with a fixed agitation of 700 rpm tomaintain an OTR of about 10 mM/h using a 5 sL/h air overlay until theOD₆₀₀ was about 8-10. After continuing growth for approximately 20 hrs,the OTR was decreased to approximately 0.2-0.7 mM/h by reducingagitation to a fixed 250-350 rpm and continued 5 sL/h airflow overlay.Measurement of the fermentor vessel off-gas by mass spectrometer wasincluded for ethanol, isobutanol, carbon dioxide, and oxygen. Continuousmeasurement of off-gas concentrations of carbon dioxide and oxygen werealso measured by a DasGip off-gas analyzer throughout the experiment.Samples were aseptically removed from the fermenter vessel throughoutthe experiment and used to measure OD₆₀₀, glucose concentration by HPLC,and isobutanol concentration in the broth by GC.

Isobutanol production reached a maximum at around 7 days with a titer ofabout 10 g/L. Yield of the fermentation, calculated when the titer ofisobutanol was between 3.7 g/L and 10 g/L, was approximately 74% maximumtheoretical. Yield of the fermentation, calculated when the titer ofisobutanol was between 0 g/L and 10 g/L, was approximately 52% maximumtheoretical. Yield of the fermentation, calculated when the titer ofisobutanol was between 0.5 g/L and 10 g/L, was approximately 61% maximumtheoretical.

Example 21 Isobutanol Production in Pdc-Gpd-Yeast

This example demonstrates isobutanol production at greater than 70%yield in a Pdc-minus, Gpd-minus member of the Saccharomyces sensustricto group, Saccharomyces clade yeast, Crabtree-positive yeast,post-WGD yeast, S. cerevisiae.

The modified yeast biocatalyst, GEVO3159, encodes a heterologous pathwayof enzymes that convert pyruvate into isobutanol. Genes for the pathwayare located on the chromosome and on a single plasmid. GEVO3159 isGEVO3124 transformed with pGV2082 (SEQ ID NO: 67), which is a high copyyeast expression plasmid used to overexpress Ec_ilvC_Q110V (Escherichiacoli ilvC containing a Q to V mutation at position 110), Ll_ilvD(Lactococcus lactis ilvD), Ll_kivD2 (Lactococcus lactis kivD), andDm_ADH (Drosophila melanogaster ADH).

The strain GEVO3124 is both GPD-deficient, PDC-deficient and able togrow in high glucose media without addition of C2-compounds. GEVO3124has integrated into the PDC1 locus the Bs_alsS1_coSc (Bacillus subtilisalsS; SEQ ID NO: 58) and LI_kivD2_coEc (Lactococcus lactis kivD, SEQ IDNO: 59) genes under the CUP1 and PGK1 promoters, respectively. Thisstrain also has the Ec_ilvC_coSc P2D1-A1 (Escherichia coli ilvC variant;SEQ ID NO: 64), LI_ilvD_coSc (Lactococcus lactis ilvD, SEQ ID NO: 65),and LI_adhA (Lactococcus lactis adhA, SEQ ID NO: 66) under the TDH3,TEF1 and ENO2 promoters, repectively, integrated into the PDC6 locus.Lastly, this strain has the Ec_ilvC_coSc_Q110V (Escherichia coli ilvCcontaining a Q to V mutation at position 110; SEQ ID NO: 61) andSc_ILV3ΔN20 (SEQ ID NO: 62) under the TDH3 and TEF1 promoters,respectively, integrated at the PDC5 locus.

GEVO3124 was generated by deletion of GPD2 using Hph as marker in strainGEVO3059. Deletion of GPD2 was carried out by transforming a hygromycinresistance marker, Hph, flanked by the GPD2 5′ and 3′ targetingsequences. This gpd2::Hph disruption cassette was generated by multiplerounds of SOE-PCR. First, the GPD2 5′ targeting sequence was amplifiedfrom pGV2164 (SEQ ID NO: 69), the CCW12 promoter was amplified frompGV1954 (SEQ ID NO: 70), the HPH ORF was amplified from pGV2074 (SEQ IDNO: 71), and the GPD2 3′ targeting sequence was also amplified. Second,the GPD2 5′ targeting sequence and the CCW12 promoter were stitchedtogether by SOE-PCR, and the Hph ORF and GPD2 3′ targeting sequence werealso stitched together by SOE-PCR. Lastly, these two SOE-PCR productswere stitched together in another round of SOE-PCR.. The resultingproduct was then transformed into GEVO3059 recovered overnight in YPD+1%EtOH+G418 or YPD+1% EtoH+G418+1 g/L glycerol, and selected onYPD+G418+Hygro+1 g/L glycerol or YPD+G418+Hygro+10 g/L glycerol plates.Twelve colonies were re-streaked for singles and colony PCRs wereperformed in single colony isolates to test for correct 5′ and 3′junctions and the loss of GPD2.

GEVO3059 was generated by deletion of GPD1 using KI_URA3 as marker instrain GEVO2994. Deletion of GPD1 was carried out by a bipartiteintegration scheme using the KI_URA3 marker. The 5′ bipartite fragmentcontained the GPD1_(—)5′ targeting sequence-T_(KI) _(—) _(URA3) _(—)_(short)-P_(FBA1)-KI_URA3_(—)3′ truncated and was generated by PCR withpGV2359 (SEQ ID NO: 72) as template. The 3′ bipartite fragment containedKI_URA3_(—)5′ truncated-T_(KI) _(—) _(URA3)-GPD1_(—)3′ targetingsequence and was generated by PCR with pGV2175 (SEQ ID NO: 73) astemplate. The 3′ truncated and 5′ truncated KI_URA3 overlapped by 347 byto allow for recombination between the KI_URA3 sequences andreconstitution of a functional K_URA3 gene. The 5′ and 3′ bipartitefragments were co-transformed into GEVO2994 and selected on SCD-U+1 g/Lglycerol plates.

GEVO2994 was generated by integrating the Ec_ilvC_coSc_P2D1-A1(Escherichia coli ilvC variant; SEQ ID NO: 64), LI_ilvD_coSc(Lactococcus lactis ilvD, SEQ ID NO: 65), and LI_adhA (Lactococcuslactis adhA, SEQ ID NO: 66) under the TDH3, TEF1 and ENO2 promoters,repectively, into the PDC6 locus of GEVO2843. GEVO2843 was generated byintegrating the Bs_alsS1_coSc (Bacillus subtilis alsS; SEQ ID NO: 58 andLI_kivD2_coEc (Lactococcus lactis kivD, SEQ ID NO: 59) into the PDC1locus of GEVO2712.

When the biocatalyst GEVO3159 was contacted with glucose in a mediumsuitable for growth of the biocatalyst, at about 30° C., the biocatalystproduced isobutanol from the glucose. A 24-hour starter culture wasstarted in a 50 mL conical tube with GEVO3159 cells from a frozenglycerol stock. The tube contained a 5 mL volume of YPD80 at a startingOD₆₀₀ of about 1.0. The starter culture was grown for approximately 24hrs in a 30° C. shaker at 250 rpm. The entire contents of the starterculture were then transferred to a flask seed culture. The flask seedculture was 80 mL of YPD80 in a 500 mL baffled Erlenmeyer flask. Theseed flask culture was grown for approximately 24 hrs in a 30° C. shakerat 250 rpm.

A portion of the flask seed culture was transferred to a 2 L DasGipfermenter containing about 750 mL of YPD80 medium to achieve a 0.5 0D₆₀₀initial cell concentration. The fermenter vessel was attached to acomputer control system to monitor and control pH at 6.0 throughaddition of base, temperature at 30° C., oxygen transfer rate (OTR), andagitation. The vessel was agitated, with a fixed agitation of 700 rpm tomaintain an OTR of about 10 mM/h using a 5 sL/h air overlay until theOD₆₀₀ was about 8-10. After continuing growth for approximately 20 hrs,the OTR was decreased to approximately 0.2-0.7 mM/h by reducingagitation to a fixed 250-350 rpm and continued 5 sL/h airflow overlay.Measurement of the fermentor vessel off-gas by mass spectrometer wasincluded for ethanol, isobutanol, carbon dioxide, and oxygen. Continuousmeasurement of off-gas concentrations of carbon dioxide and oxygen werealso measured by a DasGip off-gas analyzer throughout the experiment.Samples were aseptically removed from the fermenter vessel throughoutthe experiment and used to measure OD₆₀₀, glucose concentration by HPLC,and isobutanol concentration in the broth by GC.

Isobutanol production reached a maximum at around 5 days with a titer ofabout 8.5 g/L. Yield of the fermentation, calculated when the titer ofisobutanol was between 3.2 g/L and 8.5 g/L, was approximately 75%maximum theoretical. Yield of the fermentation, calculated when thetiter of isobutanol was between 0 g/L and 8.5 g/L, was approximately 48%maximum theoretical. Yield of the fermentation, calculated when thetiter of isobutanol was between 1 g/L and 8.5 g/L, was approximately 58%maximum theoretical.

Example 22 Isobutanol Production in Pdc-Gpd-, Co-Factor Balanced Yeast

This example demonstrates isobutanol production at greater than 70%yield in a Pdc-minus, Gpd-minus member of the Saccharomyces sensustricto group, Saccharomyces clade yeast, Crabtree-positive yeast,post-WGD yeast, S. cerevisiae, expressing an NADH-dependent isobutanolbiosynthetic pathway.

The recombinant yeast microorganism, GEVO3160, encodes a heterologousbiosynthetic pathway that converts pyruvate into isobutanol. Genes forthe pathway are located on the chromosome and on a single plasmid.GEVO3160 is GEVO3128 transformed with pGV2247(SEQ ID NO: 63), which is ahigh copy yeast expression plasmid used to overexpress Ec_ilvC_P2D1-A1(Escherichia coli ilvC variant), LI_ilvD (Lactococcus lactis ilvD),LI_kivD (Lactococcus lactis kivD), and LI_adhA (Lactococcus lactisadhA). The strain GEVO3128 is both GPD-deficient, PDC-deficient and ableto grow in high glucose media without addition of C2-compounds. GEVO3128has integrated into the PDC1 locus the Bs_alsS1_coSc (Bacillus subtilisalsS; SEQ ID NO: 58) and LI_kivD2_coEc (Lactococcus lactis kivD, SEQ IDNO: 59) genes under the CUP1 and PGK1 promoters, respectively. Thisstrain also has the Ec_ilvC_coSc_P2D1-A1 (Escherichia coli ilvC variant;SEQ ID NO: 64), LI_ilvD_coSc (Lactococcus lactis ilvD, SEQ ID NO: 65),and LI_adhA (Lactococcus lactis adhA, SEQ ID NO: 66) under the TDH3,TEF1 and ENO2 promoters, repectively, integrated into the PDC6 locus.Lastly, this strain has the Ec_ilvC_coSc_Q110V (Escherichia coli ilvCcontaining a Q to V mutation at position 110; SEQ ID NO: 61) andSc_ILV3ΔN20 (SEQ ID NO: 62) under the TDH3 and TEF1 promoters,respectively, integrated at the PDC5 locus.

GEVO3128 was generated by deletion of GPD1 using Hph as marker in strainGEVO3061. To obtain a gpd1 gpd2 double deletion, deletion of GPD1 waspursued in the gpd2::KI_URA3 deletion strains GEVO3061 Deletion of GPD1was carried out by transforming a hygromycin resistance marker, Hph,flanked by the GPD1 5′ and 3′ targeting sequences. This gpd1::Hphdisruption cassette was generated by multiple rounds of SOE PCR. First,the GPD1 5′ targeting sequence was amplified from pGV2163 (SEQ ID NO:74), the CCW12 promoter was amplified from pGV1954 (SEQ ID NO: 70), theHph ORF was amplified from pGV2074 (SEQ ID NO: 71), and the GPD1 3′targeting sequence was amplified by PCR. Second, the GPD1 5′ targetingsequence and the CCW12 promoter were stitched together by SOE-PCR, andthe Hph ORF and GPD1 3′ targeting sequence were also stitched togetherby SOE-PCR. Lastly, these two SOE-PCR products were stitched together inanother round of SOE-PCR. The resulting product was then transformedinto GEVO3061, recovered overnight in YPD+1% EtOH+G418 or YPD+1%EtOH+G418+1 g/L glycerol, and selected on YPD+G418+Hygro+1 g/L glycerolor YPD+G418+Hygro+10 g/L glycerol plates

GEVO3061 was generated by deletion of GPD2 using KI_URA3 as marker instrain GEVO2994. Deletion of GPD2 was carried out by a bipartiteintegration scheme using the KI_URA3 marker. The 5′ bipartite fragmentcontained the GPD2_(—)5′ targeting sequence-T_(KI) _(—) _(URA3) _(—)_(short)-P_(FBA1)KI_URA3_(—)3′ truncated and was generated by PCR withpGV2360 (SEQ ID NO: 75) as template. The 3′ bipartite fragment containedKI_URA3 5′ truncated-T_(KI) _(—) _(URA3)-GPD2_(—)3′ targeting sequenceand was generated by PCR with pGV2381(SEQ ID NO: 76) as a template. The3′ truncated and 5′ truncated KI_URA3 overlapped by 347 by to allow forrecombination between the KI_URA3 sequences and reconstitution of afunctional KI_URA3 gene. The 5′ and 3′ bipartite fragments wereco-transformed into GEVO2994 and selected on SCD-U+1g/L glycerol plates.

GEVO2994 was generated by integrating the Ec_ilvC_coSc_P2D1-A1(Escherichia coli ilvC variant; SEQ ID NO: 64), LI_ilvD_coSc(Lactococcus lactis ilvD, SEQ ID NO: 65), and LI_adhA (Lactococcuslactis adhA, SEQ ID NO: 66) under the TDH3, TEF1 and ENO2 promoters,repectively, into the PDC6 locus of GEVO2843. GEVO2843 was generated byintegrating the Bs_alsS1_coSc (Bacillus subtilis alsS; SEQ ID NO: 58)and LI_kivD2_coEc (Lactococcus lactis kivD, SEQ ID NO: 59) into the PDC1locus of GEVO2712.

When the biocatalyst GEVO3160 was contacted with glucose in a mediumsuitable for growth of the biocatalyst, at about 30° C., the biocatalystproduced isobutanol from the glucose. A 24-hour starter culture wasstarted in a 50 mL conical tube with GEVO3160 cells from a frozenglycerol stock. The tube contained a 5 mL volume of YPD80 medium at astarting OD₆₀₀ of about 1.0. The starter culture was grown forapproximately 24 hrs in a 30° C. shaker at 250 rpm. The entire contentsof the starter culture were then transferred to a flask seed culture.The flask seed culture was 80 mL of YPD80 medium in a 500 mL baffledErlenmeyer flask. The seed flask culture was grown for approximately 24hrs in a 30° C. shaker at 250 rpm.

A portion of the flask seed culture was transferred to a 2 L DasGipfermenter containing about 750 mL of YPD80 medium to achieve a 0.5 OD₆₀₀initial cell density. The fermenter vessel was attached to a computercontrol system to monitor and control pH at 6.0 through addition ofbase, temperature at 30° C., oxygen transfer rate (OTR), and agitation.The vessel was agitated, with a fixed agitation of 700 rpm to maintainan OTR of about 10 mM/h using a 5 sL/h air overlay until the OD₆₀₀ wasabout 8-10. After continuing growth for approximately 20 hrs, the OTRwas decreased to approximately 0.2-0.4 mM/h by reducing agitation to afixed 200 rpm and continued 5 sL/h airflow overlay. Measurement of thefermentor vessel off-gas by mass spectrometer was included for ethanol,isobutanol, carbon dioxide, and oxygen. Continuous measurement ofoff-gas concentrations of carbon dioxide and oxygen were also measuredby a DasGip off-gas analyzer throughout the experiment. Samples wereaseptically removed from the fermenter vessel throughout the experimentand used to measure OD₆₀₀, glucose concentration by HPLC, and isobutanolconcentration in the broth by GC. Isobutanol production reached amaximum at around 7 days with a titer of about 10.5 g/L.

Yield of the fermentation, calculated when the titer of isobutanol wasbetween 5.7 g/L and 10.2 g/L, was approximately 74% of theoretical (maxyield calculation). Yield of the fermentation, calculated when the titerof isobutanol was between 0 g/L and 10.5 g/L, was approximately 48% oftheoretical (yield calculation including growth of biomass). Yield ofthe fermentation, calculated when the titer of isobutanol was between0.6 g/L and 10.5 g/L, was approximately 57% of theoretical (yieldcalculation for production phase only).

Example 23 Isobutanol Production in Pdc-Gpd-Yeast

This example demonstrates isobutanol production at greater than 70%yield in a Pdc-minus, Gpd-minus member of the Saccharomyces sensustricto group, Saccharomyces clade yeast, Crabtree-positive yeast,post-WGD yeast, S. cerevisiae, expressing an NADH-dependent isobutanolbiosynthetic pathway.

The recombinant yeast microorganism, GEVO3160, encodes a heterologousbiosynthetic pathway that converts pyruvate into isobutanol. Genes forthe pathway are located on the chromosome and on a single plasmid.GEVO3160 is GEVO3128 transformed with pGV2247 (SEQ ID NO: 63), which isa high copy yeast expression plasmid used to overexpress Ec_ilvC_P2D1-A1(Escherichia coli ilvC variant), LI_ilvD (Lactococcus lactis ilvD),LI_kivD (Lactococcus lactis kivD), and LI_adhA (Lactococcus lactisadhA). The strain GEVO3128 is both GPD-deficient, PDC-deficient and ableto grow in high glucose media without addition of C2-compounds. GEVO3128has integrated into the PDC1 locus the Bs_alsS1_coSc (Bacillus subtilisalsS; SEQ ID NO: 58) and LI_kivD2_coEc (Lactococcus lactis kivD, SEQ IDNO: 59) genes under the CUP1 and PGK1 promoters, respectively. Thisstrain also has the Ec_ilvC_coSc_P2D1-A1 (Escherichia coli ilvC variant;SEQ ID NO: 64), LI_ilvD_coSc (Lactococcus lactis ilvD, SEQ ID NO: 65),and LI_adhA (Lactococcus lactis adhA, SEQ ID NO: 66) under the TDH3,TEF1 and ENO2 promoters, repectively, integrated into the PDC6 locus.Lastly, this strain has the Ec_ilvC_coSc_Q110V (Escherichia coli ilvCcontaining a Q to V mutation at position 110; SEQ ID NO: 61) andSc_ILV3ΔN20 (SEQ ID NO: 62) under the TDH3 and TEF1 promoters,respectively, integrated at the PDC5 locus.

GEVO3128 was generated by deletion of GPD1 using Hph as marker in strainGEVO3061. To obtain a gpd1 gpd2 double deletion, deletion of GPD1 waspursued in the gpd2::KI_URA3 deletion strains GEVO3061 Deletion of GPD1was carried out by transforming a hygromycin resistance marker, Hph,flanked by the GPD1 5′ and 3′ targeting sequences. This gpd1::Hphdisruption cassette was generated by multiple rounds of SOE PCR. First,the GPD1 5′ targeting sequence was amplified from pGV2163 (SEQ ID NO:74), the CCW12 promoter was amplified from pGV1954 (SEQ ID NO: 70), theHph ORF was amplified from pGV2074 (SEQ ID NO: 71), and the GPD1 3′targeting sequence was amplified by PCR. Second, the GPD1 5′ targetingsequence and the CCW12 promoter were stitched together by SOE-PCR, andthe Hph ORF and GPD1 3′ targeting sequence were also stitched togetherby SOE-PCR. Lastly, these two SOE-PCR products were stitched together inanother round of SOE-PCR. The resulting product was then transformedinto GEVO3061, recovered overnight in YPD+1% EtOH+G418 or YPD+1%EtOH+G418+1 g/L glycerol, and selected on YPD+G418+Hygro+1 g/L glycerolor YPD+G418+Hygro+10 g/L glycerol plates

GEVO3061 was generated by deletion of GPD2 using KI_URA3 as marker instrain GEVO2994. Deletion of GPD2 was carried out by a bipartiteintegration scheme using the KI_URA3 marker. The 5′ bipartite fragmentcontained the GPD2_(—)5′ targeting sequence-T_(KI) _(—) _(URA3) _(—)_(short)-P_(FBA1)KI_URA3_(—)3′ truncated and was generated by PCR withpGV2360 (SEQ ID NO: 75) as template. The 3′ bipartite fragment containedKI_URA3 5′ truncated-T_(KI) _(—) _(URA3)-GPD2_(—)3′ targeting sequenceand was generated by PCR with pGV2381 (SEQ ID NO: 76) as template. The3′ truncated and 5′ truncated KI_URA3 overlapped by 347 bp to allow forrecombination between the KI_URA3 sequences and reconstitution of afunctional KI_URA3 gene. The 5′ and 3′ bipartite fragments wereco-transformed into GEVO2994 and selected on SCD-U+1 g/L glycerolplates.

GEVO2994 was generated by integrating the Ec_ilvC_coSc_P2D1-A1(Escherichia coli ilvC variant; SEQ ID NO: 64), LI_ilvD_coSc(Lactococcus lactis ilvD, SEQ ID NO: 65), and LI_adhA (Lactococcuslactis adhA, SEQ ID NO: 66) under the TDH3, TEF1 and ENO2 promoters,repectively, into the PDC6 locus of GEVO2843. GEVO2843 was generated byintegrating the Bs_alsS1_coSc (Bacillus subtilis alsS; SEQ ID NO: 58)and LI_kivD2_coEc (Lactococcus lactis kivD, SEQ ID NO: 59) into the PDC1locus of GEVO2712.

When the biocatalyst GEVO3160 was contacted with glucose in a mediumsuitable for growth of the biocatalyst, at about 30° C., the biocatalystproduced isobutanol from the glucose. A 24-hour starter culture wasstarted in a 50 mL conical tube with GEVO3160 cells from a frozenglycerol stock. The tube contained a 5 mL volume of YPD80 medium at astarting OD₆₀₀ of about 1.0. The starter culture was grown forapproximately 24 hrs in a 30° C. shaker at 250 rpm. The entire contentsof the starter culture were then transferred to a flask seed culture.The flask seed culture was 80 mL of YPD80 medium in a 500 mL baffledErlenmeyer flask. The seed flask culture was grown for approximately 24hrs in a 30° C. shaker at 250 rpm.

A portion of the flask seed culture was transferred to a 2 L DasGipfermenter containing about 750 mL of YPD80 medium to achieve a 0.5 OD₆₀₀initial cell concentration. The fermenter vessel was attached to acomputer control system to monitor and control pH at 6.0 throughaddition of base, temperature at 30° C., oxygen transfer rate (OTR), andagitation. The vessel was agitated, with a fixed agitation of 700 rpm tomaintain an OTR of about 10 mM/h using a 5 sL/h air overlay until theOD₆₀₀ was about 8-10. After continuing growth for approximately 20 hrs,the OTR was decreased to approximately 0.3-0.8 mM/h by reducingagitation to a fixed 180-350 rpm and continued 5 sL/h airflow overlay.Measurement of the fermentor vessel off-gas by mass spectrometer wasincluded for ethanol, isobutanol, carbon dioxide, and oxygen. Continuousmeasurement of off-gas concentrations of carbon dioxide and oxygen werealso measured by a DasGip off-gas analyzer throughout the experiment.Samples were aseptically removed from the fermenter vessel throughoutthe experiment and used to measure OD₆₀₀, glucose concentration by HPLC,and isobutanol concentration in the broth by GC.

Isobutanol production reached a maximum at around 7 days with a titer ofabout 14 g/L. Yield of the fermentation, calculated when the titer ofisobutanol was between 7.2 g/L and 12.6 g/L, was approximately 71%maximum theoretical. Yield of the fermentation, calculated when thetiter of isobutanol was between 0 g/L and 14 g/L, was approximately 52%maximum theoretical. Yield of the fermentation, calculated when thetiter of isobutanol was between 0.5 g/L and 14 g/L, was approximately60% maximum theoretical.

Example 24 Isobutanol Production in Pdc-Gpd-Yeast

This example demonstrates isobutanol production at greater than 70%yield in a Pdc-minus, Gpd-minus member of the Saccharomyces sensustricto group, Saccharomyces clade yeast, Crabtree-positive yeast,post-WGD yeast, S. cerevisiae, expressing an NADH-dependent isobutanolbiosynthetic pathway.

GEVO3647 contains P_(ADH1)-Bs_alsS1_coSc (Bacillus subtilis alsS; SEQ IDNO: 58) with two copies of the Lactococcus lactis kivD gene (SEQ ID NO:59) integrated at the PDC1 locus. The strain is a transformation productof the parent strain GEVO3532 with plasmid pGV2563 (SEQ ID NO: 68).

Medium used for the fermentation was YP+80 g/L glucose+1% v/vEthanol+0.2 g/L G418. The medium was filter sterilized using a 1 Lbottle top Corning PES 0.22 μm filter (431174). Medium was pH adjusted6.0 in the fermenter vessels using 6N KOH. Table EX 15-1 outlines mediumcomponents per liter of Di-H₂O.

Inoculum cultures were started from patch plates and placing them in 500mL baffled flasks containing 80 ml YP+20 g/L glucose+1% v/v ethanol+0.2g/L G418 medium. The cultures were incubated for 32.5 h at 30° C. in anorbital shaker at 250 rpm. Cell density after incubation was as at OD₆₀₀of 2.5. Batch fermentations were conducted using a 2 L top drive motorDasGip vessel with a working volume of 1.2 L per vessel. The operatingconditions are summarized in Table EX15-1 below.

TABLE EX15-1 Process control parameters. Initial volume mL 1200Temperature ° C. 30 pH 6.0 Growth Phase (0-32 hours): Oxygen transferrate (OTR) mM/h 10.0 Air flow (overlay) slph 5.0 Agitation rpm 900Dissolved oxygen (DO) % Not controlled Production phase (32-84.3 hours):Oxygen transfer rate (OTR) mM/h 0.5 Air flow (overlay) slph 5.0Agitation rpm 300 Dissolved oxygen (DO) % Not controlled

Fermenter vessels were sterilized, along with the appropriate dissolvedoxygen probes and pH probes, for 60 minutes at 121° C. pH probes werecalibrated prior to sterilization however, dissolved oxygen probes werecalibrated post sterilization in order to achieve complete polarizationprior to calibration. Table EX15-1 outlines the process controlparameters used during the fermentation. Note that pH was controlledusing 6N KOH and 2N H₂SO₄.

The fermentation was run for 84.3 h. Vessels were sampled every 6-10 hor 3 times daily. Sterile 5 mL syringes were used to collect 3 mL offermenter broth via a sterile sample port. The sample was placed in a 2mL microfuge tube and a portion was used to measure cell density (OD₆₀₀)on a Genesys 10 spectrophotometer (Thermo Scientific). The remainingsample was filtered through a 0.22 μm Corning filter. The supernatantfrom each vessel was refrigerated in a 96-well deep well plate, andstored at 4° C. prior to gas and liquid chromatography analysis.

Analysis of volatile organic compounds, including ethanol and isobutanolwas performed on a HP 5890/6890/7890 gas chromatograph fitted with an HP7673 Autosampler, a DB-FFAP column (J&W; 30 m length, 0.32 mm ID,0.25-μM film thickness) or equivalent connected to a flame ionizationdetector (FID). The temperature program was as follows: 200° C. for theinjector, 300° C. for the detector, 100° C. oven for 1 minute, 70°C./minute gradient to 230° C., and then hold for 2.5 min. Analysis wasperformed using authentic standards (>99%, obtained from Sigma-Aldrich,and a 5-point calibration curve with 1-pentanol as the internalstandard).

Analysis of organic acid metabolites was performed on an HP-1200 HighPerformance Liquid Chromatography system equipped with two Restek RFQ150×4.6 mm columns in series. Organic acid metabolites were detectedusing an HP-1100 UV detector (210 nm) and refractive index. The columntemperature was 60° C.

This method was isocratic with 0.0180 N H₂SO₄ in Milli-Q water as mobilephase. Flow was set to 1.1 mL/min. Injection volume was 20 μM and runtime was 16 min. Analysis was performed using authentic standards (>99%,obtained from Sigma-Aldrich, with the exception of DHIV(2,3-dihydroxy-3-methyl-butanoate, CAS 1756-18-9), which was customsynthesized at Caltech (Cioffi, E. et al. Anal Biochem 104 pp. 485(1980)), and a 5-point calibration curve.

Additionally, on-line continuous measurement of the fermenter vesseloff-gas by GC-MS analysis was performed for oxygen, isobutanol, ethanol,carbon dioxide, and nitrogen throughout the experiment.

At the end of the fermentation, the isobutanol titer had reached 6.4g/L. Yield of the fermentation, calculated over the entire productionphase, i.e. from 32 to 84.3 hours, was approximately 71% of theoretical.

Example 25 Cytosolic ALS Homologs that Support Isobutanol Production

This example demonstrates isobutanol production using expression ofcytosolically localized ALS genes in the presence of the rest of theisobutanol pathway. The ALS genes were integrated into the PDC1 locus ofS. cerevisiae strain GEVO1187 and isobutanol production was achieved byexpression from plasmid of the other genes in the isobutanol pathway.Isobutanol production in strains carrying the ALS genes from T.atroviride (Ta_ALS) and T. stipitatus (Ts_ALS) was compared toisobutanol production in strains carrying the ALS gene from B. subtilis(either Bs_alsS2 or Bs_alsS1_coSc). Strains, and plasmids are listed inTables EX16-1 and EX16-2, respectively.

TABLE EX16-1 Genotype of strains disclosed herein GEVO No. Genotype Gevo1187 S. cerevisiae, CEN.PK; MATa ura3 leu2 his3 trp1 Gevo 2280 S.cerevisiae MATa ura3 leu2 his3 trp1 ADE2 pdc1::P_(CUP1-1)-Bs_AlsS2, TRP1Note that this is TRP1 +. Transformed with plasmid pGV1730. Originalisolate A2 Gevo 2618 S. cerevisiae, MATa ura3 leu2 his3 trp1pdc1::P_(CUP1-1)-Bs_AlsS1_coSc, TRP1. Transformed with plasmid pGV2114.Gevo 2621 S. cerevisiae, MATa ura3 leu2 his3 trp1pdc1::P_(CUP1-1)-Ta_Als, TRP1. Transformed with plasmid pGV2117. Gevo2622 S. cerevisiae, MATa ura3 leu2 his3 trp1 pdc1::P_(CUP1-1)-Ts_Als,TRP1. Transformed with plasmid pGV2118.

TABLE EX16-2 Plasmids disclosed herein Plasmid name Relevant Genes/UsageGenotype pGV1730 Integration plasmid that will P_(CUP1-1):Bs_alsS2, pUCORI, integrate P_(CUP1-1):Bs_alsS2 into Amp^(R), TRP1, PDC1 3′- PDC1using digestion with Nrul for fragment-Nrul-PDC1 5′- targeting. This wasthe parent fragment. vector for cloning the ALS homologs. pGV1773 Vectorwith Bacillus subtilis AlsS P_(PDC1):Bs_AlsS1_coSc, codon optimized forS. cerevisiae. P_(TDH3):Ll_kivD, P_(ADH1):Sc_ADH7_coSc, URA3 5′-end, pUCORI, kan^(R). pGV1802 DNA2.0 plasmid carrying the Ta_ALS_coSc in DNA 2.0Trichoderma atroviride ALS. vector pGV1803 DNA2.0 plasmid carrying theTs_ALS_coSc in DNA 2.0 Talaromyces stipitatus ALS. vector pGV2082 Highcopy 2μ plasmid with 4 Ec_ilvC_coSc^(Q110V), isobutanol pathway geneswithout Ll_ilvD_coSc, Ll_kivD2_coEc, an ALS gene. and Dm_ADH, 2μ ori,bla, G418R. pGV2114 Integration plasmid that willP_(CUP1-1):Bs_alsS1_coSc, pUC integrate into PDC1 using digestion ORI,Amp^(R), TRP1, PDC1 3′- with Nrul for targeting. It carries thefragment-Nrul-PDC1 5′- Bacillus subtilis AlsS gene codon fragment.optimized for S. cerevisiae. pGV2117 Integration plasmid that willP_(CUP1-1):Ta_ALS_coSc, pUC integrate into PDC1 using digestion ORI,Amp^(R), TRP1, PDC1 3′- with Nrul for targeting. It carries thefragment-Nrul-PDC1 5′- Trichoderma atroviride ALS gene fragment. codonoptimized for S. cerevisiae. pGV2118 Integration plasmid that willP_(CUP1-1):Ts_ALS_coSc, pUC integrate into PDC1 using digestion ORI,Amp^(R), TRP1, PDC1 3′- with Nrul for targeting. It carries thefragment-Nrul-PDC1 5′- Talaromyces stipitatus ALS gene fragment. codonoptimized for S. cerevisiae.

Materials and Methods for Example 25

Standard molecular biology methods for cloning and plasmid constructionwere generally used, unless otherwise noted (Sambrook, J., Russel, D. W.Molecular Cloning, A Laboratory Manual. 3^(rd) ed. 2001, Cold SpringHarbor, New York: Cold Spring Harbor Laboratory Press).

Cloning techniques included digestion with restriction enzymes, gelpurification of DNA fragments (using the Zymoclean Gel DNA Recovery Kit,Cat #D4002, Zymo Research Corp, Orange, Calif.), ligations of two DNAfragments (using the Roche rapid ligation kit, Cat #11 635 379 001,Roche Diagnostics, Mannheim, Germany), Klenow treatment of fragments togive blunt ends (using the NEB DNA Polymerase I, Large (Klenow), cat#M0210S, Ipswich, Mass.), and bacterial transformations into chemicallycompetent E. coli cells made at GEVO (TOP10). Plasmid DNA was purifiedfrom E. coli cells using the Qiagen QIAprep Spin Miniprep Kit (Cat#27106, Qiagen, Valencia, Calif.).

PCR was performed on an Eppendorf Mastercycler (Cat #71086, Novagen,Madison Wis.). The following PCR program was followed for all primersets unless otherwise noted: 94° C. for 2 min then 40 cycles of (94° C.30 sec, 54° C. 30 sec, 72° C. 1 min) then 72° C. for 10 min. Yeastcolony PCR used the FailSafe™ PCR System EPICENTRE® Biotechnologies,Madison, Wis.; Catalog #FS99250). A PCR cocktail containing 15 μl ofMaster Mix E buffer, 10.5 μl water, 2 μl of each primer at 10 μMconcentration, 0.5 μl polymerase enzyme mix from the kit was added to a0.2 mL PCR tube for each sample (30 μl each). For each candidate a smallamount of cells was added to the reaction tube using a sterile P10pipette tip. Presence of the positive PCR product was assessed usingagarose gel electrophoresis. The following primer pairs were used.Primers 1432 and 1433 for the 5′-ends of all integrations (800 by band),primers 1435 and 2233 for the 3′-ends of pGV2114 integrations (1.1 Kbband), primers 1435 and 2234 for the 3′-end of the pGV2115 integrations(1.1 Kb band), primers 1435 and 2236 for the 3′-ends of the pGV2117integrations (1.1 Kb band), primers 1435 and 2237 for the 3′-ends of thepGV2118 integrations (1.1 Kb band).

Transformation of integration plasmids was performed according to thelithium acetate protocol described above. Integration plasmids weredigested with Nrul, checked by gel electrophoresis for completedigestion and used directly from digestion. Integrative transformantswere selected by plating the transformed cells on SCD-Trp agar medium.Once the transformants were single colony purified they were maintainedon SCD-Trp plates. Once transformants were screened by PCR as describedabove for proper integration, each strain was transformed with theplasmid pGV2082. Transformants were plated to YPD plates containing 0.2g/L G418.

SCD-Trp: 20 g/L glucose, 14 g/L Sigma™ Synthetic Dropout Mediasupplement (includes amino acids and nutrients excluding histidine,tryptophan, uracil, and leucine), and 6.7 g/L Difco™ Yeast NitrogenBase. 0.076 g/L histidine, 0.380 g/L leucine, and 0.076 g/L uracil.

Fermentations

Strains with integrated ALS genes expressed from the CUP1 promoter weretransformed with pGV2082 (which carries the other 4 isobutanol pathwaygenes Ec_ilvC_coScQ110V (SEQ ID NO: 61), LI_ilvD (SEQ ID NO: 65),LI_kivd2_coEc (SEQ ID NO: 59), and Dm_ADH (SEQ ID NO: 60)). Strains werepatched onto YPD plates containing 0.2 mg/mL G418. The following morningcells were removed from the plate with a sterile toothpick andresuspended in 4 mL of YPD with 0.2 mg/mL G418. The OD₆₀₀ was determinedfor each culture. Cells were added to 50 mL YP with 5% dextrose and 0.2mg/mL G418 such that a final OD₆₀₀ of 0.1 was obtained. 1 mL of mediawas removed and the OD₆₀₀ for this undiluted sample determined, leftovermedia was stored at 4° C. to act as media blank for the analyticssubmission, and to act as the t=0 sample for the fermentation. At t=24h, 2 mL of media was removed and 25 μM used at a 1:40 dilution todetermine OD₆₀₀. The remaining culture was centrifuged in amicrocentrifuge at maximum speed for 10 min and a 1:10 dilution read onthe YSI. 50% glucose containing 0.2 mg/mL G418 was added to a finalconcentration of 100 g/L glucose. 1 mL of supernatant was analyzed bygas chromatography as described above. At t=48 h, 2 mL of media wasremoved and 25 μM used at a 1:40 dilution to determine OD₆₀₀. Theremaining culture was centrifuged in a microcentrifuge at maximum speedfor 10 min and a 1:10 dilution read on the YSI. 50% glucose plus water(with 0.2 mg/mL G418) were added to give a final concentration ofglucose of 100 g/L. 1 mL of supernatant was analyzed by gaschromatography. At t=72 h, 2 mL of media was removed and 25 μL used at a1:40 dilution to determine OD₆₀₀. The remaining culture was centrifugedin a microcentrifuge at maximum speed for 10 min and a 1:10 dilutionread on the YSI. 1 mL of supernatant was analyzed by gas chromatographyand high performance liquid chromatography.

Yeast Strain Construction

GEVO2280 was constructed by transforming GEVO1187 with the integrationplasmid pGV1730. The plasmid pGV1730 was first linearized with Nrul,which cuts such that the linear plasmid will integrate into the PDC1locus, and the DNA was transformed using the standard yeasttransformation protocol. Transformants were selected by plating toSCGaI-Trp plates. Individual integrants were verified using colony PCRwith primers 1432 and 1433 to detect proper integration at the 5′-end(803 by fragment) and primers 1220 and 1435 to detect proper integrationat the 3′-end (772 bp).

GEVO2618 was constructed by transforming GEVO1187 with the integrationplasmid pGV2114. The plasmid was first linearized with Nrul, which cutssuch that the linear plasmid will integrate into the PDC1 locus, and theDNA was transformed using the standard yeast transformation protocoldescribed above. Correct integration was verified with colony PCR usingprimers 1432 and 1433 to check the 5′-end of the integration (800 byband) and primers 1435 and 2233 for the 3′-end of pGV2114 integration(1,100 by band).

GEVO2621 was constructed by transforming GEVO1187 with the integrationplasmid pGV2117. The plasmid was first linearized with Nrul, which cutssuch that the linear plasmid will integrate into the PDC1 locus, and theDNA was transformed using the standard yeast transformation protocoldescribed above. integration was verified with colony PCR using primers1432 and 1433 to check the 5′-end of the integration (800 by band) andprimers 1435 and 2236 for the 3′-end of pGV2117 integration (1,100 byband).

GEVO2622 was constructed by transforming GEVO1187 with the integrationplasmids pGV2118. The plasmid was first linearized with Nrul, which cutssuch that the linear plasmid will integrate into the PDC1 locus, and theDNA was transformed using the standard yeast transformation protocoldescribed above. Twelve transformants were single colony purified.Correct integration was verified with colony PCR using primers 1432 and1433 to check the 5′-end of the integration (800 by band) and primers1435 and 2237 for the 3′-end of pGV2118 integration (1,100 by band).

Each ALS-containing strain was transformed with the 4 component pathwayplasmid, pGV2082 (SEQ ID NO: 67), as described above. Control strainsGEVO2280 (Bs_alsS2) and GEVO1187 (no ALS) were also transformed withpGV2082. Transformants were single colony purified and maintained on YPDplates with 0.2 mg/mL G418.

Plasmid Construction

Construction of plasmid pGV2082. The plasmid pGV2044 carries the genesEc_ilvC_coSc^(Q110V), Bs_AlsS2, LI_ilvD_coSc and Dm_ADH. The plasmidpGV2082 was created from pGV2044 by replacing the Bs_AlsS2 withLI_kivD2_coEc as follows: the LI_kivD2_coEc gene and associated PGK1promoter were removed from pGV2047 by digestion with AwII and NcoI. The2530 by fragment was purified by gel electrophoresis and the fragmentwas prepared using the Zymoclean kit described above. Plasmid pGV2044was digested with EcoRI and SbfI to remove the Bs_AlsS2 gene andassociated CUP1 promoter and the 11275 by vector fragment was gelpurified. The vector and insert were treated with Klenow fragment toproduce blunt ends. The pGV2044 vector fragment and theP_(PGK1):LI_kivD2_coEc insert were ligated using standard methods in anapproximately 5:1 insert:vector molar ratio and transformed into TOP10chemically competent E. coli cells. Plasmid DNA was isolated and correctclones were confirmed using restriction enzyme analysis consisting ofdigestion of potential clones with the following enzymes: EcoRV to givecorrect fragments of 6.3 and 7.5 kb, EcoRV plus Nrul to give correctfragments of 2.9, 3.4, and 7.5 kb), EcoRI plus NcoI to give correctfragments of 2.5 and 11.2 Kb.

pGV1730 was digested with BamHI and SalI and the vector fragment of 4.9kb was gel purified by agarose gel electrophoresis. pGV1773 was digestedwith BamHI and SalI and the 1.7 Kb fragment containing the Bs_AlsS_coScwas gel purified by agarose gel electrophoresis. The pGV1730 vectorfragment was ligated to the pGV1773 insert fragment using the Rocherapid ligation kit in a ratio of 5:1 insert to vector ratio andtransformed into TOP10 chemically competent E. coli cells. Plasmid DNAwas isolated and correct clones were confirmed using restriction enzymeanalysis consisting of digestion of potential clones with Scal plus PstIto give correct fragments of 2.7, 1.7, 1.4 and 0.9 Kb, AflII to givecorrect fragments of 1.5 and 5.1 kb, NaeI plus StuI to give correctfragments of 1.4, 5.2 kb.

Construction of pGV2117: pGV1730 was digested with BamHI and SalI andthe vector fragment of 4.9 kb was gel purified by agarose gelelectrophoresis. pGV1802 was digested with BamHI and SalI and the 1.8 kbfragment containing the Ta_ALS was gel purified by agarose gelelectrophoresis. The pGV1730 vector fragment w:as ligated to the pGV1802insert fragment using the Roche rapid ligation kit in a ration of 5:1insert to vector ratio and transformed into TOP-10 chemically competentE.coli cells. Plasmid DNA was isolated and correct clones were confirmedusing restriction enzyme analysis consisting of digestion of potentialclones with BamHl plus Stul to give correct fragments of 1.4 and 5.2 kb,SalI plus PstI to give correct fragments of 0.7 and 5.9 kb, and AhdI togive correct fragments of 1.9 and 4.7 kb.

Construction of pGV2118: pGV1730 was digested with BamHI and SalI andthe vector fragment of 4.9 kb was gel purified by agarose gelelectrophoresis. pGV1803 was digested with BamHI and SalI and the 1.8 kbfragment containing the Ts_ALS gel purified by agarose gelelectrophoresis. The pGV1730 vector fragment was ligated to the pGV1803insert fragment using the Roche rapid ligation kit in a ration of 5:1insert to vector ratio and transformed into TOP-10 chemically competentE.coli cells. Plasmid DNA was isolated and correct clones were confirmedusing restriction enzyme analysis consisting of digestion of potentialclones with NaeI to give correct bands of 2.9 and 3.7 kb, EcoRV to givecorrect bands of 0.7 and 5.9 kb, and HpaI plus SacI to give correctbands of 1.9 and 4.7 kb.

Results

Fermentations of GEVO1187, GEVO2280, GEVO2618, GEVO2621, GEVO2622 andtransformed with pGV2082 were carried out as described above (exceptG418 was not added to the glucose at 24 h). In this experiment strainscontaining the ALS genes Ta_ALS_coSc and Ts_ALS_coSc produced moreisobutanol than the strain containing the Bs_Als2. The Bs_Als1_coScproduced the most isobutanol. Table EX16-3 shows the final OD, glucoseconsumption, and isobutanol titer for each of the strains. Theintegration of the cytosolic genes Ta_ALS_coSc and Ts_ALS_coSc led toproduction of isobutanol that was in each case 6-fold above that of astrain without an integrated ALS gene, demonstrating that these strainsare producing isobutanol using a cytosolic pathway.

TABLE EX16-3 Results of fermentation with cytosolic ALS homologs, at 72h Glucose Isobutanol Strain OD₆₀₀ consumed g/L produced g/L GEVO118710.9 ± 0.3  233 ± 36 0.3 ± 0.0 GEVO2280 9.9 ± 0.3 274 ± 26  1.3 ± 0.11GEVO2618 9.4 ± 0.2 138 ± 9  2.6 ± .09 GEVO2621 9.9 ± 0.3 161 ± 52 1.9 ±.18 GEVO2622 10.8 ± 0.6  182 ± 47 1.8 ± .15

The foregoing detailed description has been given for clearness ofunderstanding only and no unnecessary limitations should be understoodthere from as modifications will be obvious to those skilled in the art.

While the invention has been described in connection with specificembodiments thereof, it will be understood that it is capable of furthermodifications and this application is intended to cover any variations,uses, or adaptations of the invention following, in general, theprinciples of the invention and including such departures from thepresent disclosure as come within known or customary practice within theart to which the invention pertains and as may be applied to theessential features hereinbefore set forth and as follows in the scope ofthe appended claims.

The disclosures, including the claims, figures and/or drawings, of eachand every patent, patent application, and publication cited herein arehereby incorporated herein by reference in their entireties.

1. A recombinant yeast microorganism comprising an isobutanol producingmetabolic pathway, wherein said isobutanol producing metabolic pathwaycomprises the following substrate to product conversions: (i) pyruvateto acetolactate; (ii) acetolactate to 2,3-dihydroxyisovalerate; (iii)2,3-dihydroxyisovalerate to a-ketoisovalerate; (iv) a-ketoisovalerate toisobutyraldehyde; and (v) isobutyraldehyde to isobutanol; wherein therecombinant yeast microorganism comprises: (a) an NADH-dependentketol-acid reductoisomerase to catalyze the conversion of acetolactateto 2,3-dihydroxyisovalerate using NADH as a cofactor; and (b) anNADH-dependent alcohol dehydrogenase to catalyze the conversion ofisobutyraldehyde to isobutanol using NADH as a cofactor, wherein therecombinant yeast microorganism has been engineered to disrupt, mutate,or delete one or more endogenous pyruvate decarboxylase (PDC) genes, andwherein said recombinant yeast microorganism has reduced endogenous PDCactivity as compared to the corresponding yeast microorganism that hasnot been engineered to have reduce endogenous PDC activity.
 2. Therecombinant yeast microorganism of claim 1, wherein said one or moreendogenous PDC genes is selected from the group consisting of PDC1,PDC2, PDC5, and PDC6.
 3. The recombinant yeast microorganism of claim 1,wherein said recombinant yeast microorganism is engineered to disrupt,mutate, or delete one or more endogenous glycerol-3-phosphatedehydrogenase (GPD) genes.
 4. The recombinant yeast microorganism ofclaim 3, wherein said one or more endogenous GPD genes is selected fromthe group consisting of GPD1 and GPD2.
 5. The recombinant yeastmicroorganism of claim 1, wherein said recombinant yeast microorganismis engineered to disrupt an endogenous pyruvate dehydrogenase (PDH)gene.
 6. The recombinant yeast microorganism of claim 1, wherein saidrecombinant yeast microorganism is engineered or selected to grow onglucose independently of C2-compounds at a growth rate substantiallyequivalent to the growth rate of the corresponding yeast microorganismthat has not been engineered to have reduced endogenous PDC activity. 7.The recombinant yeast microorganism of claim 1, wherein the conversionof pyruvate to acetolactate is catalyzed by an acetolactate synthase. 8.The recombinant yeast microorganism of claim 7, wherein saidacetolactate synthase is a cytosolically-localized acetolactatesynthase.
 9. The recombinant yeast microorganism of claim 8, whereinsaid cytosolically-localized acetolactate synthase is encoded by theLactococcus lactis alsS gene.
 10. The recombinant yeast microorganism ofclaim 8, wherein said cytosolically-localized acetolactate synthase isencoded by the Bacillus subtilis alsS gene.
 11. The recombinant yeastmicroorganism of claim 1, wherein the conversion of2,3-dihydroxyisovalerate to isobutyraldehyde is catalyzed by a dihydroxyacid dehydratase.
 12. The recombinant yeast microorganism of claim 11,said dihydroxy acid dehydratase is encoded by the Lactococcus lactisilvD gene.
 13. The recombinant yeast microorganism of claim 1, whereinthe conversion of α-ketoisovalerate to isobutyraldehyde is catalyzed bya 2-keto-acid decarboxylase.
 14. The recombinant yeast microorganism ofclaim 13, wherein said 2-keto-acid decarboxylase is encoded by theLactococcus lactis kivD gene.
 15. The recombinant yeast microorganism ofclaim 1, wherein said recombinant yeast microorganism producesisobutanol at a yield which is at least 70% of the theoretical yield ofisobutanol from glucose.
 16. The recombinant yeast microorganism ofclaim 1, wherein the recombinant yeast microorganism is a yeast of theSaccharomyces clade.
 17. The recombinant yeast microorganism of claim16, wherein said yeast of the Saccharomyces clade is Saccharomycescerevisiae.
 18. A method of producing isobutanol, comprising: (a)providing the recombinant yeast microorganism according to claim 1; and(b) cultivating the recombinant yeast microorganism in a culture mediumcontaining a feedstock providing the carbon source, until the isobutanolis produced.
 19. The method of claim 18, wherein isobutanol is producedunder anaerobic or microaerobic conditions.
 20. The method of claim 18,wherein isobutanol is produced at a yield which is at least 70% of thetheoretical yield of isobutanol from glucose.